Discordance among gene trees across genomes is an important feature of organisms . and outlined h... more Discordance among gene trees across genomes is an important feature of organisms . and outlined how individual gene trees may disagree as a result of processes such as incomplete lineage sorting (ILS), reticulation, horizontal gene transfer, gene duplication, and paralogy. Of these, ILS has received the most attention and is predicted to be particularly relevant in species that have large effective population sizes, low mutation rates, long generation times, or that have undergone rapid radiations . Reticulation through hybridization or organellar capture has also been documented as playing an important role in gene-tree discordance . Pines are long lived and have large effective population sizes, making them an ideal group for studying ILS . They are also wind pollinated, with weak barriers to interspecific gene flow, permitting hybridization to increase the proportion of alleles shared by reproductively compatible species . Pinus subsection Australes Loudon comprises ~30 pine species of outstanding ecological and economic importance distributed in North and Central America and the Greater Antilles (Farjon, 2010; Fig. ). The subsection can be subdivided into three groups (Table ). The first, colloquially known as the California closedcone pines, comprises three species with serotinous cones from western North America. Here, we refer to the group informally as the Attenuatae. erected Pinus subsection
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...
SummaryThe scarlet runner bean is an open-pollinated legume from the highlands of Mesoamerica tha... more SummaryThe scarlet runner bean is an open-pollinated legume from the highlands of Mesoamerica that is cultivated in small-scale agriculture for its dry seeds and immature pods. 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 SNVs) 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 though there is evidence of a severe initial genetic bottleneck, followed by a population expansion. Introgression from wild to domesticated populations was detected, but not in the opposite direction. This asymmetric introgression might contribute to the recovery of ...
The widespread use of genomic tools has allowed for a deeper understanding of the genetics and th... more The widespread use of genomic tools has allowed for a deeper understanding of the genetics and the evolutionary dynamics of domestication. Recent studies have suggested that multiple domestications and introgression are more common than previously thought. However, the ability to correctly infer the many aspects of domestication process depends on having an adequate representation of wild relatives. Cultivated maize (Zea maysssp.mays) is one of the most important crops in the world, with a long and a relatively well-documented history of domestication. The current consensus points towards a single domestication event from teosinteZea maysssp.parviglumisfrom the Balsas Basin in Southwestern Mexico. However, the underlying diversity of teosintes fromZ. maysssp. parviglumisandZea maysssp.mexicanawas not taken into account in early studies. We used 32 739 single nucleotide polymorphisms (SNPs) obtained from 29 teosinte populations and 43 maize landraces to explore the relationship betwe...
In the last decade, genomics and the related fields of transcriptomics and epigenomics have revol... more In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.
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...
Fifty-one isolates of Rhizobium leguminosarum biovar phaseoli from various geographic and ecologi... more Fifty-one isolates of Rhizobium leguminosarum biovar phaseoli from various geographic and ecological sources, largely in Mexico, were characterized by the electrophoretic mobilities of 15 metabolic enzymes, and 46 distinctive multilocus genotypes (electrophoretic types [ETs]) were distinguished on the basis of allele profiles at the enzyme loci. Mean genetic diversity per enzyme locus among the 46 ETs was 0.691, the highest value yet recorded for any species of bacterium. The occurrence of strong nonrandom associations of alleles over loci suggested a basically clonal population structure, reflecting infrequent recombination of chromosomal genes. Multilocus genotypic diversity was unusually high, with the most strongly differentiated pairs of ETs having distinctive alleles at all 15 loci and major clusters of ETs diverging at genetic distances as large as 0.89. This great diversity in the chromosomal genome raises the possibility that R. leguminosarum biovar phaseoli is a polyphylet...
Proceedings of the National Academy of Sciences, 2019
Mexico is recognized as the center of origin and domestication of maize. Introduction of modern m... more Mexico is recognized as the center of origin and domestication of maize. Introduction of modern maize varieties (MVs) into Mexico raised concerns regarding the possible effects of gene flow from MVs into maize landraces (LRs) and their wild relatives (WRs), teosintes. However, after more than 60 y from the release of the first MVs, the impact of the sympatry with LRs and their WRs has not been explored with genetic data. In this work, we assessed changes in the genomes of 7 maize LRs and 2 WR subspecies from collections spanning over 70 y. We compared the genotypes obtained by genotyping by sequencing (GBS) for LRs and WRs before and after the adoption of MVs, and observed introgression from sympatric MVs into LRs and into the WR Zea mays ssp. mexicana sampled after the year 2000. We also found a decrease in the paired divergence index ( F ST ) between MV-LR and MV-WR over the same time frame. Moreover, we determined that LR genetic diversity increased after 2000, probably as a resu...
Domestication has been influenced by formal plant breeding since the onset of intensive agricultu... more Domestication has been influenced by formal plant breeding since the onset of intensive agriculture and the Green Revolution. Despite providing food security for some regions, intensive agriculture has had substantial detrimental consequences for the environment and does not fulfill smallholder's needs under most developing countries conditions. Therefore, it is necessary to look for alternative plant production techniques, effective for each environmental, socio-cultural, and economic conditions. This is particularly relevant for countries that are megadiverse and major centers of plant domestication and diversification. In this white paper, a Mexico-centered initiative is proposed, with two main objectives: (1) to study, understand, conserve, and sustainably use the genetic diversity of domesticated plants and their wild relatives, as well as the ongoing evolutionary processes that generate and maintain it; and (2) to strengthen food and forestry production in a socially fair ...
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...
Tropical mountains are areas of high species richness and endemism. Two historical phenomena may ... more Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky islands (the Trans-Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation ca...
Background: Homoplasy affects demographic inference estimates. This effect has been recognized an... more Background: Homoplasy affects demographic inference estimates. This effect has been recognized and corrective methods have been developed. However, no studies so far have defined what homoplasy metrics best describe the effects on demographic inference, or have attempted to estimate such metrics in real data. Here we study how homoplasy in chloroplast microsatellites (cpSSR) affects inference of population expansion time. cpSSRs are popular markers for inferring historical demography in plants due to their high mutation rate and limited recombination. Results: In cpSSRs, homoplasy is usually quantified as the probability that two markers or haplotypes that are identical by state are not identical by descent (Homoplasy index, P). Here we propose a new measure of multi-locus homoplasy in linked SSR called Distance Homoplasy (DH), which measures the proportion of pairwise differences not observed due to homoplasy, and we compare it to P and its per cpSSR locus average, which we call Mean Size Homoplasy (MSH). We use simulations and analytical derivations to show that, out of the three homoplasy metrics analyzed, MSH and DH are more correlated to changes in the population expansion time and to the underestimation of that demographic parameter using cpSSR. We perform simulations to show that Approximate Bayesian Computation (ABC) can be used to obtain reasonable estimates of MSH and DH. Finally, we use ABC to estimate the expansion time, MSH and DH from a chloroplast SSR dataset in Pinus caribaea. To our knowledge, this is the first time that homoplasy has been estimated in population genetic data. We show that MSH and DH should be used to quantify how homoplasy affects estimates of population expansion time. We also demonstrate how ABC provides a methodology to estimate homoplasy in population genetic data.
In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a... more In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into "landraces." Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples. In order to investigate the genomic foundation of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina MaizeSNP50 BeadChip) obtained from 50 samples representing five maize landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico), and searched for markers suitable for landrace assignment. Landrace clusters could not be identified taking all the genomic information, but they become manifest taking only a subset of SNPs with high FST am...
Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examp... more Repeated DNA sequences are a general characteristic of eucaryotic genomes. Although several examples of DNA reiteration have been found in procaryotic organisms, only in the case of the archaebacteria Halobacterium halobium and Halobacterium volcanii [C. Sapienza and W. F. Doolittle, Nature (London) 295:384-389, 1982], has DNA reiteration been reported as a common genomic feature. The genomes of two Rhizobium phaseoli strains, one Rhizobium meliloti strain, and one Agrobacterium tumefaciens strain were analyzed for the presence of repetitive DNA. Rhizobium and Agrobacterium spp. are closely related soil bacteria that interact with plants and that belong to the taxonomical family Rhizobiaceae. Rhizobium species establish a nitrogen-fixing symbiosis in the roots of legumes, whereas Agrobacterium species is a pathogen in different plants. The four strains revealed a large number of repeated DNA sequences. The family size was usually small, from 2 to 5 elements, but some presented more ...
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.
The environmental variables that define a species ecological niche should be associated with the ... more The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with ad...
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 . En este regis-FRAGMENTACIÓN Y EXPANSIÓN DEMOGRÁFICA
The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as wel... more The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (H E = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (H E = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.
Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to reco... more Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plan...
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Papers by Daniel Piñero