Daniel Piñero

• National Autonomous University of Mexico

Abiotic factors are important for defining population structure and limiting gene flow, especially in ectotherm species. In amphibians, abiotic factors like temperature and precipitation can either facilitate or restrict gene flow. The challenge is identifying if these factors can lead to a pattern of isolation by environment. Our study aims to qua...

In North America, the genetic diversity of Abies, Picea, Pinus, and Pseudotsugahas been analyzed with molecular markers of codominant and dominant nature, using information from mitochondrial, chloroplast, and nuclear genomes. The objective of this studywas to review the recent research assessing the genetic diversity of Pinaceae in North America (...

Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri-urban forests. A notable case are fir(Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 polluti...

Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly as tropospheric ozone (O3), which contributes to the decline of urban and peri‐urban forests. A notable case are fir (Abies religiosa) forests in the peripheral mountains southwest of Mexico City, which have been severely affected by O3 pollut...

Background: The Trans-Mexican Volcanic Belt (TMVB) in central Mexico is characterized by peaks of high altitude and geologic instability. In this zone, Pinus strobiformis and Pinus ayacahuite form a contact zone with Pinus veitchii. The taxonomical circumscription of white pines in Central Mexico has been unstable, especially regarding the status o...

Specificity in plant–pathogen gene‐for‐gene (GFG) interactions is determined by the recognition of pathogen proteins by the products of plant resistance (R) genes. The evolutionary dynamics of R genes in plant–virus systems is poorly understood. We analyse the evolution of the L resistance locus to tobamoviruses in the wild pepper Capsicum annuum v...

Membracis mexicana (Hemiptera: Membracidae) is distributed in four biogeographic provinces of Mexico. Field observations indicate that there are different forms of this species, but the distribution of the phenotype and the genetic variation of this species have not been clarified. The aim of this study was to quantify the phenotypic and genetic va...

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...

Urbanization modifies ecosystem conditions and evolutionary processes. This includes air pollution, mostly tropospheric ozone (O3), which leads to urban and peri-urban forest decline. Such is the case of fir (Abies religiosa) forests in the peripheral mountains west of Mexico City, which have been severely affected by O3 pollution since the 1970s....

To identify which abiotic factors are most important for defining population structure, both spatiotemporal scales and species-specific life history attributes and ecology must be accounted for. Our study aim is to quantify the extent to which divergence is driven by abiotic factors such as temperature, precipitation and elevation. To do so, we use...

Simple Summary Chitons are a charismatic group of mollusks that live underneath rocks on shores throughout the world, where they experience variations due to environmental factors. Temperature may cause animals to grow to a larger size in colder climates, a trend originally ascribed to endothermic animals. In this work, advanced techniques were use...

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...

Climate changes, together with geographical barriers imposed by the Sierra Madre Oriental and the Chihuahuan Desert, have shaped the genetic diversity and spatial distribution of different species in northern Mexico. Pinus pinceana Gordon & Glend. tolerates extremely arid conditions. Northern Mexico became more arid during the Quaternary, modifying...

Empirical studies have shown that several taxa exhibit a decoupled relationship between lineage species diversification (the balance between speciation and extinction) and phenotypic diversification. This has been recognized by some authors as fundamental evidence for non-adaptive radiation. In the leaf-toed geckos Phyllodactylus of North America,...

The Mexican fruit fly, Anastrepha ludens, is an important pest that causes widespread damage to a number of fruit crops in Mexico. The sterile insect technique (SIT) is commonly used for its control. However, the existence of natural barriers can give rise to a population structure in neutral loci and possibly behavioral or adaptive traits that int...

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, fe...

Context: Gene flow in riparian ecosystems is influenced by landscape features such as orography, climate, and salinity. The 'downstream increase in genetic diversity' (DIGD) hypothesis states that the unidirectionality of the watercourse causes an accumulation of genetic diversity towards downstream populations, while upstream populations are more...

El género Phyllodactylus esta ampliamente representado en la región insular del Golfo de California (GC). En comparación con sus parientes continentales, los Phyllodactylus insulares se distribuyen en poblaciones aisladas y con tamaños efectivos (Ne) reducidos, lo que posiblemente ha favorecido su divergencia en alopatría. Bajo estas circunstancias...

Background In 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;...

Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants...

Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants...

Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes‐level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species‐level diversity, and higher. However, empirical data is still limited, wi...

Eradication of herbivores, due to human disturbances, produces a demographic outburst of highly competitive prey species, which in turn reduces plant species diversity. This happens at Los Tuxtlas tropical rainforest, Mexico, where a population outburst of the understory palm Astrocaryum mexicanum is ostensibly excluding tree species, but how this...

• 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 fin...

Aim To (a) evaluate whether colonization of newly emerged high-elevation habitats occurred from neighbouring highlands (allopatric divergence and niche conservatism) or from within the same mountain (peripatric or parapatric divergence and niche shift) and (b) test for the effect of past landscape configurations in geographically structuring biodiv...

Key message We reconstructed the needle tissue Transcriptome of P. pinceana for individuals from distinct biogeographic regions across a temperature and precipitation gradient that represents its natural distribution. Gene expression analysis via RNA-Seq identified differential response to biotic stress. Abstract Phenotypic plasticity includes phy...

Leaf-toed geckos (Phyllodactylus) exhibit much cryptic diversity, at least in North America. However, the origins of Central American taxa and their relationships with North American congeners remain unknown. The P. tuberculosus species complex is ideal for evolutionary and biogeographic studies because its geographic distribution extends from nort...

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 t...

The current unprecedented rates of environmental perturbation, particularly in rain forest ecosystems, are jeopardizing the persistence of a variety of tropical species. The development of adequate conservation programs requires incorporating the evolutionary history and population genetic information of species, especially in those threatened by h...

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...

Montane ecosystems occur throughout the world, and harbor many endemic species. They also provide key ecological services, including the catchment of water resources and the storage of organic carbon. These ecosystems are vulnerable to global climate change and increasing human pressures, including forestry and their conversion to arable land. In t...

In tropical sky-islands, cold-affinity populations tend to become isolated at highlands during the interglacial periods, and to expand into the lowlands where they become more connected during the glacial periods. Although this has been widely studied in trees, it is poorly understood how fungal symbionts can differentiate among mountains (allopatr...

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 none...

We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using...

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...

México es un centro de origen de la agricultura y domesticación de plantas. Como resultado, más de 130 cultivos son originarios de México y forman parte de un profundo entramado biocultural que permite realizar agricultura en un amplio rango de condiciones ambientales. Esta agrobiodiversidad emergió del proceso de la evolución bajo domesticación, e...

Mexico is a center of origin for agriculture and plant domestication. As a result, more than 130 crops are native to Mexico, forming part of a deep biocultural network and allowing agriculture to take place in a wide range of environmental conditions. This agrobiodiversity emerged from the process of evolution under domestication, which occurred si...

Genetic variation within- and divergence among-populations is essential for conservation and management efforts. In plants that are dispersed mainly by ocean currents, physical features of the landscape may influence rates of gene flow among populations by preventing or facilitating dispersal of buoyant propagules. The complex landscape and the pat...

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 th...

Aim: To 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. Location: Central Mexico. Methods: We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (A...

The deforestation and degradation of natural habitats is the second largest contributor to carbon dioxide (CO2) emissions to the atmosphere. Temperate forests cover ∼16.5% of the Mexican landscape, and are a priority ecosystem for global conservation due to their high rate of endemism and species diversity. These forests also provide valuable ecosy...

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 whole-genome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scru...

Aim Historical and geological events can impact the genetic structure of species, producing signatures that vary among taxa and among gene pools within taxa. Such signatures can also be affected by local geography and tolerance to environmental conditions. However, disentangling the different drivers of population structure is often difficult. In a...

The diverse offspring of clonal species differ in their dispersability, influencing genotypic diversity and clonal structure. Here, we determined dispersal patterns and their impact on genetic structure in Opuntia microdasys, a self‐incompatible cactus with three dispersal units (one sexual and two clonal). We analyzed dispersal, using experiments...

Premise of the Study Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long‐lived, wind‐pollinated plants with large population sizes and weak reproductive barriers. Methods We used solution hybridization for targeted enrichment and massi...

Aim To assess if geographical and/or environmental factors are driving skull morphology and genetic structure in the cosmopolitan bat species, Tadarida brasiliensis. Location North, Central and South America, Greater and Lesser Antilles. Methods We analysed morphometric, genetic and environmental data from the entire distribution of T. brasiliens...

Background – Pinus caribaea Morelet comprises three varieties of tropical pines distributed in the Caribbean Basin: P. caribaea var. hondurensis, var. caribaea, and var. bahamensis. The insular and continental distribution of these varieties, as well as the geological processes in the region, have been important factors for analysing evolutionary p...

Blastocystis 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 sprea...

List of the sequences reported in the present study and those previously reported within the literature.

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. Th...

The family Curculionidae (Coleoptera), the "true" weevils, have diversified tightly linked to the evolution of flowering plants. Here, we aim to assess diversification at a lower taxonomic level. We analyze the evolution of the genus Trichobaris in association with their host plants. Trichobaris comprises eight to thirteen species; their larvae fee...

The study of maize domestication has overlooked the genetic structure within maize’s wild relative teosinte. Prior to investigating the domestication history of maize ( Zea mays subspecies mays ), one should first understand the population history of teosintes and how they relate to maize. To achieve this, we used 32,739 SNPs obtained from a broad...

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-t...

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 chlorop...

The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In th...

p>Background: The domestication process has left signatures in the genomes of domesticated species. Before the existence of molecular markers, only phenotypic traits could be used in domestication studies and breeding programs, but these approaches required long time and effort. In the last decades, the use of molecular markers dramatically increas...

This work presents a review of the use of enzymes as molecular markers for evolutionary studies, in particular population genetics. First, the methodology of starch electrophoresis is shown as a useful tool To detect variation within and among populations. Second, applications to evolutionary biology are presented. In plants these markers have been...

Understanding host-pathogen interactions requires analyses to address the multiplicity of scales in heterogeneous landscapes. Anthropogenic influence on plant communities, especially cultivation, is a major cause of environmental heterogeneity. We have approached the analysis of how environmental heterogeneity determines plant-virus interactions by...

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, tha...

p>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 Est...

In their commentary on our recent paper (Martínez-Ramos et al. 2016), Arroyo-Rodríguez and Melo (2016, hereafter referred to as A-R&M) present imprecisions that need clarification to avoid misleading the readership of FEE regarding the contribution of our paper.

This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in...

Chiltepin populations analysed and number of pvr2/eIF4E1 sequences obtained in this study. (DOCX)

Genetic diversity of pvr2/eIF4E1 exons and introns in chiltepin populations according to geographical provinces and habitats. (DOCX)

Zygosity at the pvr2/eIF4E1 locus and identification of susceptible and resistant plants in chiltepin populations. (DOCX)

Effects of the mutations identified in pvr2/eIF4E1 protein on the pvr2/eIF4E1-VPg:PVY interactions evaluated. Yeast growth was evaluated by yeast two hybrid assays and was expressed by percentage of the yeast growth on the selective medium (-LWH) compared to the reference yeast colonies co-transformed with pGADT7::pvr2+ and pGBKT7::VPg-PVY; standar...

Geographic and genetic distance in wild chiltepin populations at the pvr2/eIF4E1 locus. Log-transformed data are presented. (TIF)

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum based only on the third positions of the codons. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 are pvr2/eIF...

Frequency of heterozygous plants for the pvr2/eIF4E1 coding sequences in chiltepin populations according to geographical provinces and habitats. (DOCX)

Genetic differentiation of the pvr2/eIF4E1 coding sequences between biogeographical provinces. (DOCX)

Complementation of yeast strain JO55 with pvr2/eIF4E1 coding sequences identified in chiltepin populations. Control -: negative control corresponding to yeast colonies transformed with empty p424GBP/TRP1 plasmids. (TIF)

Sequence alignment of pvr2/eIF4E1 alleles identified in chiltepin populations and localisation of the polymorphic positions (orange), sites involved in the Potyvirus resistance (purple) and in the m7GTP binding cap recognition (green) and domain of eIF4G interaction (blue). (TIF)

Phylogenetic relationships between Capsicum annuum pvr2+ allele and 4 crystallized eIF4E (A), comparison of the secondary structure of these proteins (B) and disorder prediction in the pvr2/eIF4E1 protein (C). *: localisation of the polymorphic positions identified in the pvr2/eIF4E1 protein of chiltepins. (TIF)

Superposition of the 3D-model generated independently of the pvr2/eIF4E1 alleles identified in chiltepin populations. (A) superposition of the models; (B) pvr2+ (green) and pvr1+ (orange), superposition: RMSDbackbone = 1.050 Å; (C) pvr2+ (green) and pvr21 (orange), superposition: RMSDbackbone = 1.107 Å; (D) pvr2+ (green) and pvr22 (orange), superpo...

Phylogenetic relationships between Potyvirus species and location of the potyviruses infecting chiltepin populations. The presented phylogeny was reconstructed based on partial NIb (304nt) by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. Grey boxes mentioned the potyvirus sequences identified in chiltepin populations...

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 are pvr2/eIF4E1 haplotypes described in [23]; pvr1+, pvr1 an...

Differences in the VPg protein sequence between TEV and TEV-like potyviruses. TEV (Consensus): Consensus sequence obtained with 20 world-wide TEV isolates (accession numbers: L38714, M11458, M15239.1, NC_001555.1, DQ986288.1, EF470242.2, JN711120.1, EU334794.1, EU334793.1, EU334792.1, EU334791.1, EU334790.1, 334789.1, EU334788.1, EU334787.1, EU3347...

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum based on the first and the second positions of the codons. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 ar...

Anthropogenic disturbances affecting tropical forest reserves have been documented, but their ecological long-term cumulative effects are poorly understood. Habitat fragmentation and defaunation are two major anthropogenic threats to the integrity of tropical reserves. Based on a long-term (four decades) study, we document how these disturbances sy...