Daniel Piñero - Academia.edu (original) (raw)

Papers by Daniel Piñero

Research paper thumbnail of Environmental heterogeneity shapes physiological traits in tropical direct‐developing frogs

Ecology and Evolution

Tropical ectotherm species tend to have narrower physiological limits than species from temperate... more Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms. Here, we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct‐developing frog (Craugastor loki) in a tropical gradient. We address the following questions: (a) Does preferred temperature vary with elevation and among bioclimatic domains? (b) Do thermal tolerance limits, that is, critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains? and (c) Are ...

Research paper thumbnail of Helmet Shape and Phylogeography of the Treehopper Membracis mexicana

Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mex... more Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mexico, field observations indicate that there are different forms of this species but so far it has not been recorded how the different forms are and how they are distributed. The aim of this study was to quantify the phenotypic and genetic variation of M. mexicana and determine if the config-uration of biogeographic provinces impacts the distribution of this variation. To do this we ana-lyzed 307 photographs using 19 landmarks and geometric morphometrics to quantify the pheno-typic variation in helmets. We sequenced five molecular markers for 205 individuals to describe the phylogeographic pattern. As a result, we identified three morphological configurations of the helmet of M. mexicana and two genetic lineages. The morphotypes are 1) large and wide helmet with small dorsal spots, 2) small and narrow helmet with large dorsal spots, and 3) small and narrow helmet with small spots. Genetic...

Research paper thumbnail of Bergmann’s Rule under Rocks: Testing the Influence of Latitude and Temperature on a Chiton from Mexican Marine Ecoregions

Biology

Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder cli... more Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder climates are found. In the Mexican Pacific, three marine ecoregions are distinguishable across a latitudinal gradient. Stenoplax limaciformis is an abundant chiton species that is distributed on rocky shores in these ecoregions. Geometric morphometric analyses were performed to describe the shape and size variation of S. limaciformis between marine ecoregions that vary in sea surface temperature with latitude, thus testing Bergmann’s rule. Individuals’ body shape ranged from elongated to wide bodies. Although there was variation in chitons’ body shape and size, the was no evidence of allometry among localities. The Gulf of California is the northernmost ecoregion evaluated in this work, where larger chitons were observed and lower sea surface temperature values were registered. The results suggest that S. limaciformis follows a trend to Bergmann’s rule, such as endotherms. These mollusks do...

Research paper thumbnail of Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico

PeerJ

Background Genetic diversity is fundamental for the survival of species. In particular, in a clim... more Background Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity. Methods We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a g...

Research paper thumbnail of Exploring the relation between genetic structure and habitat heterogeneity in the rodent Liomys pictus from Chamela, Jalisco

ACTA ZOOLÓGICA MEXICANA (N.S.)

Local populations of the spiny pocket mice, Liomys pictus, were sampled from the tropical deciduo... more Local populations of the spiny pocket mice, Liomys pictus, were sampled from the tropical deciduous and semideciduous forests from Chamela, Jalisco, Mexico, where L. pictus experiences profound population fluctuations and high rates of population turnover, associated with the strong environmental seasonality and heterogeneity characteristic of these forests. In order to review the hypothesis stating that the level of genebetween subpopulations from these two contrasting habitats were evaluated. Thirty presumptive gene loci were analyzed using starch-gel electrophoresis. Allele frequencies, number of heterozygous loci and observed and expected heterozygosity values were not statistically different between subpopulations. Population differences and sex-biased dispersal were also evaluated with an assignment test based on individual genotypes. Seventy-two percent of individuals were correctly assigned to their population of origin, which we considered indicative of low interpopulation ...

Research paper thumbnail of The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

Evolution Letters

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. ... more The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even th...

Research paper thumbnail of A single genealogical lineage from the Sonoran Desert and the Mexican Pacific Coast explains the haplotype distribution of Trichobaris compacta

Revista Mexicana de Biodiversidad, 2021

The weevil Trichobaris compacta occurs in southwest USA where it uses Datura wrightii as host pla... more The weevil Trichobaris compacta occurs in southwest USA where it uses Datura wrightii as host plant and to oviposit into its fruits. Previously, we showed that T. compacta can use 4 other Datura species as host plants also, but the mitochondrial lineages of T. compacta do not appear to be specifically associated to any Datura species. Thus, given that T. compacta is distributed from the southwest USA up to the Tehuantepec Isthmus in the Pacific coast ranges of Mexico, we aimed to determine how the genetic variation of T. compacta is distributed along the geographical space. To determine how geography has shaped the genetic population structure of T. compacta we used a 663-bp region of the COI gene in a sample of 232 individuals from 29 different localities. We detected 49 haplotypes, one of which is widely distributed. The un-rooted haplotype network and phylogeny showed that T. compacta integrates one single lineage. Also, the population genetic structure of T. compacta is made up ...

Research paper thumbnail of Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

Scientific Reports, 2021

Tropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and ev... more Tropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and evolved as chemical defenses against herbivores and pathogens in the annual herb Datura stramonium (Solanaceae). Here, we present the first draft genomes of two plants from contrasting environments of D. stramonium. Using these de novo assemblies, along with other previously published genomes from 11 Solanaceae species, we carried out comparative genomic analyses to provide insights on the genome evolution of D. stramonium within the Solanaceae family, and to elucidate adaptive genomic signatures to biotic and abiotic stresses in this plant. We also studied, in detail, the evolution of four genes of D. stramonium—Putrescine N-methyltransferase, Tropinone reductase I, Tropinone reductase II and Hyoscyamine-6S-dioxygenase—involved in the tropane alkaloid biosynthesis. Our analyses revealed that the genomes of D. stramonium show signatures of expansion, physicochemical divergence and/or posit...

Research paper thumbnail of Co-structure analysis and genetic associations reveal insights into pinworms (Trypanoxyuris) and primates (Alouatta palliata) microevolutionary dynamics

BMC Ecology and Evolution, 2021

BackgroundIn parasitism arm race processes and red queen dynamics between host and parasites reci... more BackgroundIn parasitism arm race processes and red queen dynamics between host and parasites reciprocally mold many aspects of their genetics and evolution. We performed a parallel assessment of population genetics and demography of two species of pinworms with different degrees of host specificity (Trypanoxyuris multilabiatus, species-specific; andT. minutus,genus-specific) and their host, the mantled howler monkey (Alouatta palliata), based on mitochondrial DNA sequences and microsatellite loci (these only for the host). Given that pinworms and primates have a close co-evolutionary history, covariation in several genetic aspects of their populations is expected.ResultsMitochondrial DNA revealed two genetic clusters (West and East) in both pinworm species and howler monkeys, although population structure and genetic differentiation were stronger in the host, while genetic diversity was higher in pinworms than howler populations. Co-divergence tests showed no congruence between host...

Research paper thumbnail of Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum

Applied and Environmental Microbiology, 1991

The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determi... more The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes. Nonsymbiotic strains were isolated from the rhizosphere of bean plants and characterized by growth on differential media and at different temperatures, intrinsic antibiotic resistance, the lack of homology to a nifH probe, and their inability to form nodules on bean roots. All the isolates clustered with R. leguminosarum bv. phaseoli reference strains and did not encompass any other Rhizobium taxa. Their rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were also found to be identical to those of R. leguminosarum bv. phaseoli reference strains. When complemented with an R. leguminosarum bv. phaseoli symbiotic plasmid (p42d), the nonsymbiotic isolates were able to fix nitrogen in symbiosis with bean roots at levels similar to those of the parental strain. Th...

Research paper thumbnail of Sistemática Filogeográfica y sus Aplicaciones a la Evolución y Conservación de los Bosques de Coníferas en México: El Caso de Pinus montezumae y P. pseudostrobus

Acta Universitaria, 2002

El análisis de la genealogía de alelos o haplotipos ha revolucionado en la última década el estud... more El análisis de la genealogía de alelos o haplotipos ha revolucionado en la última década el estudio de la estructura genética de las poblaciones. En la actualidad no solamente se puede estudiar la cantidad de variación genética en una población, sino también se pueden inferir los procesos que históricamente son responsables de esa estructura genética. Este enfoque está apoyado por la teoría de coalescencia que analiza los patrones de divergencia de alelos o haplotipos bajo diferentes supuestos no sólo relacionados con los aspectos genéticos de las poblaciones sino también con los aspectos demográficos históricos. Estas innovaciones al estudio de la estructura genética tienen impacto en al menos dos grandes áreas de la biología evolutiva. La primera de ellas tiene que ver con los aspectos de conservación de regiones que albergan a las especies estudiadas para generar estrategias de conservación más acorde con los procesos históricos por los que han pasado las especies. La segunda de ...

Research paper thumbnail of Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

Ecology and Evolution, 2019

AimTo infer the geological and climatic factors that have shaped the genetic diversity and struct... more AimTo infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico.LocationCentral Mexico.MethodsWe collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA.ResultsBoth cpDNA and n...

Research paper thumbnail of The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita

Molecular Plant, 2019

Whole-genome duplications are an important source of evolutionary novelties that change the mode ... more Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a wholegenome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including a newly assembled genome of Cucurbita argyrosperma, and compared the gene contents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.

Research paper thumbnail of {"__content__"=>"Genetic Diversity and Distribution of Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico.", "i"=>{"__content__"=>"Blastocystis"}}

BioMed research international, 2018

subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomat... more subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of ST3 from other regions of the planet. Our analyses reveled that diversity of ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a commo...

Research paper thumbnail of What is a genus in the Trypanosomatidae family? Phylogenetic analysis of two small rRNA sequences

Molecular Biology and Evolution, 1991

Research paper thumbnail of Estudios demográficos en plantas. Astrocaryum mexicanum Liebm. 1. Estructura de las poblaciones

Botanical Sciences, 2016

Este trabajo es el inicial de una serie de estudios demográficos sobre Astrocaryum mexicanum que ... more Este trabajo es el inicial de una serie de estudios demográficos sobre Astrocaryum mexicanum que se encuentra en desarrollo desde 1975. En él se describe la estructura de las poblaciones de A. mexicanum , así como la composición florística arbórea de seis sitios permanentes de observación de 600 m2, situados en la selva alta perennifolia de la Estación de Biología Tropical Los Tuxtlas en el Estado de Veracruz, México. Para las poblaciones de A. mexicanum se analizan la distribución de alturas, radios de copa y número de hojas vivas, estableciéndose las relaciones estructurales entre los sitios. En lo que se refiere a la distribución de alturas (dado que hemos encontrado una relación directa entre altura y edad), cuatro de los sitios tienen una distribución "normal" de edades, mientras que los otros dos muestran alteraciones, probablemente debidas a sobrevivencias diferenciales de ciertas clases de edad. Para las comunidades vegetales de los sitios se analizó la composición...

Research paper thumbnail of Genomic instability in Rhizobium phaseoli

Journal of Bacteriology, 1988

Experience from different laboratories indicates that Rhizobium strains can generate variability ... more Experience from different laboratories indicates that Rhizobium strains can generate variability in regard to some phenotypic characteristics such as colony morphology or symbiotic properties. On the other hand, several reports suggest that under certain stress conditions or genetic manipulations Rhizobium cells can present genomic rearrangements. In search of frequent genomic rearrangements, we analyzed three Rhizobium strains under laboratory conditions that are not considered to cause stress in bacterial populations. DNAs from direct descendants of a single cell were analyzed in regard to the hybridization patterns obtained, using as probes different recombinant plasmids or cosmids; while most of the probes utilized did not show differences in the hybridization patterns, some of them revealed the occurrence of frequent genomic rearrangements. The implications and possible biological significance of these observations are discussed.

Research paper thumbnail of Range expansion and fragmentation in Mexican populations of Pinus ayacahuite

Boletin De La Sociedad Botanica De Mexico, Dec 1, 2008

E l género Pinus incluye aproximadamente 110 especies, de las cuales alrededor del 50% habitan en... more E l género Pinus incluye aproximadamente 110 especies, de las cuales alrededor del 50% habitan en México, haciendo de este país el de mayor diversidad de este género en el mundo. Las palinofl oras del Terciario en México registran la presencia más antigua de pinos en el norte de este país en el Oligoceno. Durante el Mioceno se encuentra a los géneros Pinus y Picea en lo que actualmente es el estado de Veracruz, aunque con una representación muy pobre. Es durante el Plioceno que tanto la abundancia como la diversidad de los elementos de fl ora neártica aumentan hacia el sur de México y Centroamérica (Graham, 1999). En este regis

Research paper thumbnail of Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

Research paper thumbnail of Phylogenetics ofPinus(Pinaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Region Sequences

Molecular Phylogenetics and Evolution, 1999

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in... more A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (‫؍‬subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these ''New World hard pines,'' which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained. 1999 Academic Press

Research paper thumbnail of Environmental heterogeneity shapes physiological traits in tropical direct‐developing frogs

Ecology and Evolution

Tropical ectotherm species tend to have narrower physiological limits than species from temperate... more Tropical ectotherm species tend to have narrower physiological limits than species from temperate areas. As a consequence, tropical species are considered highly vulnerable to climate change since minor temperature increases can push them beyond their physiological thermal tolerance. Differences in physiological tolerances can also be seen at finer evolutionary scales, such as among populations of ectotherm species along elevation gradients, highlighting the physiological sensitivity of such organisms. Here, we analyze the influence of elevation and bioclimatic domains, defined by temperature and precipitation, on thermal sensitivities of a terrestrial direct‐developing frog (Craugastor loki) in a tropical gradient. We address the following questions: (a) Does preferred temperature vary with elevation and among bioclimatic domains? (b) Do thermal tolerance limits, that is, critical thermal maximum and critical thermal minimum vary with elevation and bioclimatic domains? and (c) Are ...

Research paper thumbnail of Helmet Shape and Phylogeography of the Treehopper Membracis mexicana

Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mex... more Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mexico, field observations indicate that there are different forms of this species but so far it has not been recorded how the different forms are and how they are distributed. The aim of this study was to quantify the phenotypic and genetic variation of M. mexicana and determine if the config-uration of biogeographic provinces impacts the distribution of this variation. To do this we ana-lyzed 307 photographs using 19 landmarks and geometric morphometrics to quantify the pheno-typic variation in helmets. We sequenced five molecular markers for 205 individuals to describe the phylogeographic pattern. As a result, we identified three morphological configurations of the helmet of M. mexicana and two genetic lineages. The morphotypes are 1) large and wide helmet with small dorsal spots, 2) small and narrow helmet with large dorsal spots, and 3) small and narrow helmet with small spots. Genetic...

Research paper thumbnail of Bergmann’s Rule under Rocks: Testing the Influence of Latitude and Temperature on a Chiton from Mexican Marine Ecoregions

Biology

Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder cli... more Bergmann’s rule relates the trend of increasing body size with higher latitudes, where colder climates are found. In the Mexican Pacific, three marine ecoregions are distinguishable across a latitudinal gradient. Stenoplax limaciformis is an abundant chiton species that is distributed on rocky shores in these ecoregions. Geometric morphometric analyses were performed to describe the shape and size variation of S. limaciformis between marine ecoregions that vary in sea surface temperature with latitude, thus testing Bergmann’s rule. Individuals’ body shape ranged from elongated to wide bodies. Although there was variation in chitons’ body shape and size, the was no evidence of allometry among localities. The Gulf of California is the northernmost ecoregion evaluated in this work, where larger chitons were observed and lower sea surface temperature values were registered. The results suggest that S. limaciformis follows a trend to Bergmann’s rule, such as endotherms. These mollusks do...

Research paper thumbnail of Conservation genomics of Agave tequilana Weber var. azul: low genetic differentiation and heterozygote excess in the tequila agave from Jalisco, Mexico

PeerJ

Background Genetic diversity is fundamental for the survival of species. In particular, in a clim... more Background Genetic diversity is fundamental for the survival of species. In particular, in a climate change scenario, it is crucial that populations maintain genetic diversity so they can adapt to novel environmental conditions. Genetic diversity in wild agaves is usually high, with low genetic differentiation among populations, in part maintained by the agave pollinators such as the nectarivorous bats. In cultivated agaves, patterns of genetic diversity vary according to the intensity of use, management, and domestication stage. In Agave tequilana Weber var. azul (A. tequilana thereafter), the plant used for tequila production, clonal propagation has been strongly encouraged. These practices may lead to a reduction in genetic diversity. Methods We studied the diversity patterns with genome-wide SNPs, using restriction site associated DNA sequencing in cultivated samples of A. tequilana from three sites of Jalisco, Mexico. For one locality, seeds were collected and germinated in a g...

Research paper thumbnail of Exploring the relation between genetic structure and habitat heterogeneity in the rodent Liomys pictus from Chamela, Jalisco

ACTA ZOOLÓGICA MEXICANA (N.S.)

Local populations of the spiny pocket mice, Liomys pictus, were sampled from the tropical deciduo... more Local populations of the spiny pocket mice, Liomys pictus, were sampled from the tropical deciduous and semideciduous forests from Chamela, Jalisco, Mexico, where L. pictus experiences profound population fluctuations and high rates of population turnover, associated with the strong environmental seasonality and heterogeneity characteristic of these forests. In order to review the hypothesis stating that the level of genebetween subpopulations from these two contrasting habitats were evaluated. Thirty presumptive gene loci were analyzed using starch-gel electrophoresis. Allele frequencies, number of heterozygous loci and observed and expected heterozygosity values were not statistically different between subpopulations. Population differences and sex-biased dispersal were also evaluated with an assignment test based on individual genotypes. Seventy-two percent of individuals were correctly assigned to their population of origin, which we considered indicative of low interpopulation ...

Research paper thumbnail of The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean (Phaseolus coccineus L.)

Evolution Letters

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. ... more The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even th...

Research paper thumbnail of A single genealogical lineage from the Sonoran Desert and the Mexican Pacific Coast explains the haplotype distribution of Trichobaris compacta

Revista Mexicana de Biodiversidad, 2021

The weevil Trichobaris compacta occurs in southwest USA where it uses Datura wrightii as host pla... more The weevil Trichobaris compacta occurs in southwest USA where it uses Datura wrightii as host plant and to oviposit into its fruits. Previously, we showed that T. compacta can use 4 other Datura species as host plants also, but the mitochondrial lineages of T. compacta do not appear to be specifically associated to any Datura species. Thus, given that T. compacta is distributed from the southwest USA up to the Tehuantepec Isthmus in the Pacific coast ranges of Mexico, we aimed to determine how the genetic variation of T. compacta is distributed along the geographical space. To determine how geography has shaped the genetic population structure of T. compacta we used a 663-bp region of the COI gene in a sample of 232 individuals from 29 different localities. We detected 49 haplotypes, one of which is widely distributed. The un-rooted haplotype network and phylogeny showed that T. compacta integrates one single lineage. Also, the population genetic structure of T. compacta is made up ...

Research paper thumbnail of Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

Scientific Reports, 2021

Tropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and ev... more Tropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and evolved as chemical defenses against herbivores and pathogens in the annual herb Datura stramonium (Solanaceae). Here, we present the first draft genomes of two plants from contrasting environments of D. stramonium. Using these de novo assemblies, along with other previously published genomes from 11 Solanaceae species, we carried out comparative genomic analyses to provide insights on the genome evolution of D. stramonium within the Solanaceae family, and to elucidate adaptive genomic signatures to biotic and abiotic stresses in this plant. We also studied, in detail, the evolution of four genes of D. stramonium—Putrescine N-methyltransferase, Tropinone reductase I, Tropinone reductase II and Hyoscyamine-6S-dioxygenase—involved in the tropane alkaloid biosynthesis. Our analyses revealed that the genomes of D. stramonium show signatures of expansion, physicochemical divergence and/or posit...

Research paper thumbnail of Co-structure analysis and genetic associations reveal insights into pinworms (Trypanoxyuris) and primates (Alouatta palliata) microevolutionary dynamics

BMC Ecology and Evolution, 2021

BackgroundIn parasitism arm race processes and red queen dynamics between host and parasites reci... more BackgroundIn parasitism arm race processes and red queen dynamics between host and parasites reciprocally mold many aspects of their genetics and evolution. We performed a parallel assessment of population genetics and demography of two species of pinworms with different degrees of host specificity (Trypanoxyuris multilabiatus, species-specific; andT. minutus,genus-specific) and their host, the mantled howler monkey (Alouatta palliata), based on mitochondrial DNA sequences and microsatellite loci (these only for the host). Given that pinworms and primates have a close co-evolutionary history, covariation in several genetic aspects of their populations is expected.ResultsMitochondrial DNA revealed two genetic clusters (West and East) in both pinworm species and howler monkeys, although population structure and genetic differentiation were stronger in the host, while genetic diversity was higher in pinworms than howler populations. Co-divergence tests showed no congruence between host...

Research paper thumbnail of Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum

Applied and Environmental Microbiology, 1991

The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determi... more The genetic structure of a population of nonsymbiotic Rhizobium leguminosarum strains was determined by the electrophoretic mobilities of eight metabolic enzymes. Nonsymbiotic strains were isolated from the rhizosphere of bean plants and characterized by growth on differential media and at different temperatures, intrinsic antibiotic resistance, the lack of homology to a nifH probe, and their inability to form nodules on bean roots. All the isolates clustered with R. leguminosarum bv. phaseoli reference strains and did not encompass any other Rhizobium taxa. Their rRNA operon restriction fragment length polymorphisms and the nucleotide sequence of a fragment of the 16S rRNA gene were also found to be identical to those of R. leguminosarum bv. phaseoli reference strains. When complemented with an R. leguminosarum bv. phaseoli symbiotic plasmid (p42d), the nonsymbiotic isolates were able to fix nitrogen in symbiosis with bean roots at levels similar to those of the parental strain. Th...

Research paper thumbnail of Sistemática Filogeográfica y sus Aplicaciones a la Evolución y Conservación de los Bosques de Coníferas en México: El Caso de Pinus montezumae y P. pseudostrobus

Acta Universitaria, 2002

El análisis de la genealogía de alelos o haplotipos ha revolucionado en la última década el estud... more El análisis de la genealogía de alelos o haplotipos ha revolucionado en la última década el estudio de la estructura genética de las poblaciones. En la actualidad no solamente se puede estudiar la cantidad de variación genética en una población, sino también se pueden inferir los procesos que históricamente son responsables de esa estructura genética. Este enfoque está apoyado por la teoría de coalescencia que analiza los patrones de divergencia de alelos o haplotipos bajo diferentes supuestos no sólo relacionados con los aspectos genéticos de las poblaciones sino también con los aspectos demográficos históricos. Estas innovaciones al estudio de la estructura genética tienen impacto en al menos dos grandes áreas de la biología evolutiva. La primera de ellas tiene que ver con los aspectos de conservación de regiones que albergan a las especies estudiadas para generar estrategias de conservación más acorde con los procesos históricos por los que han pasado las especies. La segunda de ...

Research paper thumbnail of Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

Ecology and Evolution, 2019

AimTo infer the geological and climatic factors that have shaped the genetic diversity and struct... more AimTo infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico.LocationCentral Mexico.MethodsWe collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA.ResultsBoth cpDNA and n...

Research paper thumbnail of The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita

Molecular Plant, 2019

Whole-genome duplications are an important source of evolutionary novelties that change the mode ... more Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a wholegenome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including a newly assembled genome of Cucurbita argyrosperma, and compared the gene contents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.

Research paper thumbnail of {"__content__"=>"Genetic Diversity and Distribution of Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico.", "i"=>{"__content__"=>"Blastocystis"}}

BioMed research international, 2018

subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomat... more subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of ST3 from other regions of the planet. Our analyses reveled that diversity of ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a commo...

Research paper thumbnail of What is a genus in the Trypanosomatidae family? Phylogenetic analysis of two small rRNA sequences

Molecular Biology and Evolution, 1991

Research paper thumbnail of Estudios demográficos en plantas. Astrocaryum mexicanum Liebm. 1. Estructura de las poblaciones

Botanical Sciences, 2016

Este trabajo es el inicial de una serie de estudios demográficos sobre Astrocaryum mexicanum que ... more Este trabajo es el inicial de una serie de estudios demográficos sobre Astrocaryum mexicanum que se encuentra en desarrollo desde 1975. En él se describe la estructura de las poblaciones de A. mexicanum , así como la composición florística arbórea de seis sitios permanentes de observación de 600 m2, situados en la selva alta perennifolia de la Estación de Biología Tropical Los Tuxtlas en el Estado de Veracruz, México. Para las poblaciones de A. mexicanum se analizan la distribución de alturas, radios de copa y número de hojas vivas, estableciéndose las relaciones estructurales entre los sitios. En lo que se refiere a la distribución de alturas (dado que hemos encontrado una relación directa entre altura y edad), cuatro de los sitios tienen una distribución "normal" de edades, mientras que los otros dos muestran alteraciones, probablemente debidas a sobrevivencias diferenciales de ciertas clases de edad. Para las comunidades vegetales de los sitios se analizó la composición...

Research paper thumbnail of Genomic instability in Rhizobium phaseoli

Journal of Bacteriology, 1988

Experience from different laboratories indicates that Rhizobium strains can generate variability ... more Experience from different laboratories indicates that Rhizobium strains can generate variability in regard to some phenotypic characteristics such as colony morphology or symbiotic properties. On the other hand, several reports suggest that under certain stress conditions or genetic manipulations Rhizobium cells can present genomic rearrangements. In search of frequent genomic rearrangements, we analyzed three Rhizobium strains under laboratory conditions that are not considered to cause stress in bacterial populations. DNAs from direct descendants of a single cell were analyzed in regard to the hybridization patterns obtained, using as probes different recombinant plasmids or cosmids; while most of the probes utilized did not show differences in the hybridization patterns, some of them revealed the occurrence of frequent genomic rearrangements. The implications and possible biological significance of these observations are discussed.

Research paper thumbnail of Range expansion and fragmentation in Mexican populations of Pinus ayacahuite

Boletin De La Sociedad Botanica De Mexico, Dec 1, 2008

E l género Pinus incluye aproximadamente 110 especies, de las cuales alrededor del 50% habitan en... more E l género Pinus incluye aproximadamente 110 especies, de las cuales alrededor del 50% habitan en México, haciendo de este país el de mayor diversidad de este género en el mundo. Las palinofl oras del Terciario en México registran la presencia más antigua de pinos en el norte de este país en el Oligoceno. Durante el Mioceno se encuentra a los géneros Pinus y Picea en lo que actualmente es el estado de Veracruz, aunque con una representación muy pobre. Es durante el Plioceno que tanto la abundancia como la diversidad de los elementos de fl ora neártica aumentan hacia el sur de México y Centroamérica (Graham, 1999). En este regis

Research paper thumbnail of Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

Research paper thumbnail of Phylogenetics ofPinus(Pinaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Region Sequences

Molecular Phylogenetics and Evolution, 1999

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in... more A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (‫؍‬subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these ''New World hard pines,'' which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained. 1999 Academic Press