Juan Núñez-Farfán

Verified

Juan verified their affiliation via an institutional email.

Learn more

Verified

Juan verified their affiliation via an institutional email.

Learn more

• Doctor in Ecology
• Professor (Full) at National Autonomous University of Mexico

Host race formation in phytophagous insects can be an early stage of adaptive speciation. However, the evolution of phenotypic plasticity in host use is another possible outcome. Using a reciprocal transplant experiment we tested the hypothesis of local adaptation in the aphid Brevicoryne brassicae. Aphid genotypes derived from two sympatric host p...

Abstract. -It has been assumed that herbivores constitute a selective agent for the evolution of plant resistance. However, few studies have tested this hypothesis. In this study, we look at the annual weed Datura stramonium for evidence of current natural selection for resistance to her- bivorous insects. Paternal half-sib families obtained throug...

The consequences of selfing and outcrossing in Datura stramonium, a colonizing annual species, were experimentally assessed in terms of the fecundity of maternal plants and the performance of their progeny. Selfed and cross-pollinated plants were produced through controlled crosses and were then planted in their native environment. We recorded size...

Tolerance and resistance are two different plant defense strategies against herbivores. Empirical evidence in natural populations reveals that individual plants allocate resources simultaneously to both strategies, thus plants exhibit a mixed pattern of defense. In this review we examine the conditions that promote the evolutionary stability of mix...

The studies of Clausen, Keck, and Hiesey (CKH) have been widely cited as exemplars of ecotypic differentiation in textbooks and in the primary literature. However, the scope of their findings and achievements is significantly greater than this. In this paper we analyze the research program of CKH, highlighting their major findings during the years...

Background Natural enemies of herbivore insects can change the arms race between plants and insects. Their presence and abundance even can affect the co-evolution of interacting species. The annual herb Datura stramonium varies geographically in the extent of its direct defenses against herbivores. Its main specialist herbivore, Lema daturaphila ,...

The genomic evolution of pathogens associated with cancer in humans represents a fascinating yet underexplored area in evolutionary research. In this chapter, we will elucidate how a complex eco-evolutionary interaction unfolds between hosts and pathogens. Additionally, we provide a comprehensive exploration and holistic overview of the evolutionar...

An introduction to a novel habitat represents a challenge to plants because they likely would face new interactions and possibly different physical context. When plant populations arrive to a new region free from herbivores, we can expect an evolutionary change in their defense level, although this may be contingent on the type of defense, resistan...

Differential expression of genes is key to mediating developmental and stress‐related plant responses. Here, we addressed the regulation of plant metabolic responses to biotic stress and the developmental variation of defense‐related genes in four species of the genus Datura with variable patterns of metabolite accumulation and development. We comb...

Background: Podostemaceae is the largest family of strictly aquatic angiosperms. Species of this family possess unusual morphological and reproductive characters, grow attached to rocks in rivers with strong currents, and have a life cycle tightly linked to seasonality. Due to its reduced floral structures, which characterizes most species, the ana...

Plant resistance refers to the heritable ability of plants to reduce damage caused by natural enemies, such as herbivores and pathogens, either through constitutive or induced traits like chemical compounds or trichomes. However, the genetic architecture ⎯ the number and genome location of genes that affect plant defense and the magnitude of their...

When colonizing new ranges, plant populations may benefit from the absence of the checks imposed by the enemies, herbivores, and pathogens that regulated their numbers in their original range. Therefore, rates of plant damage or infestation by natural enemies are expected to be lower in the new range. Exposing both non-native and native plant popul...

The expression of plant resistance traits against arthropod herbivores often comes with costs to other essential plant functions such as growth and fitness. These trade-offs are shaped by the allocation of limited resources. However, plants might also possess the capability to allocate resources to both resistance and growth, thereby ensuring their...

Knowing how species and communities respond to environmental change is fundamental in the context of climate change. The search for patterns of abundance and phenotypic variation along altitudinal gradients can provide evidence on adaptive limits. We evaluated the species abundance and the variation in morphometric and stomatal characters in five t...

Macroevolutionary patterns in the association between plant species and their herbivores result from ecological divergence promoted by, among other factors, plants’ defenses and nutritional quality, and herbivore adaptations. Here, we assessed the performance of the herbivores Lema trilineata daturaphila, a trophic specialist on Datura, and Spodopt...

Multiple factors threaten the conservation of crop wild relatives (CWR), such as habitat transformation and fragmentation, rapid environmental changes, introduction of invasive species, urbanization, and introduction of genetically modified organisms. Moreover, in regions where CWR coexist with their domesticated counterparts, reductions of genetic...

Agricultural losses brought about by insect herbivores can be reduced by understanding the strategies that plants use against insect herbivores. The two main strategies that plants use against herbivory are resistance and tolerance. They are, however, predicted to be mutually exclusive, yet numerous populations have them both (hence a mixed defense...

Elucidating the diversification process of congeneric species makes it necessary to identify the factors promoting species variation and diversification. Comparative gene family analysis allows us to elucidate the evolutionary history of species by identifying common genetic/genomic mechanisms underlying species responses to biotic and abiotic envi...

Besides recruitment and dispersal, fruits are key resources for the maintenance of insect communities. This study is focused on the insects inhabiting the fruits of 4 wild Lauraceae species. Although the trees of this family are important elements of tropical forests, their interaction with insects, especially in association with fruits, remains po...

Premise: Although ecological differentiation driven by altitude and soil is hypothesized to promote coexistence of sympatric tree species of Damburneya (Lauraceae), the mechanistic role of leaf functional variation on ecological differentiation among co-occurring species remains unexplored. We aimed to determine whether the patterns of leaf trait...

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...

Adaptive evolution enhances the fitness of populations via the natural selection of genetic variants. Phenotypic plasticity may also increase fitness but it can be neutral or even maladaptive. In natural environments, water and light are factors that generate plastic responses of plants. The purpose of this study was to analyze the adaptive phenoty...

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban...

The niche-centroid hypothesis states that populations that are distributed near the centroid of the species' ecological niche will have higher fitness-related attributes, such as population abundance and genetic diversity than populations near the edges of the niche. Empirical evidence based on abundance and, more recently, genetic diversity data s...

In recent years, evidence has been found that plant-pollinator interactions are altered by land-use and that genetic diversity also plays a role. However, how land-use and genetic diversity influence plant-pollinator interactions, particularly in the Neotropics, where many endemic plants exist is still an open question. Cucurbita pepo is a monoecio...

Premise: The mechanisms generating the geographical distributions of genetic diversity are a central theme in evolutionary biology. The amount of genetic diversity and its distribution are controlled by several factors, including dispersal abilities, physical barriers, and environmental and climatic changes. We investigated the patterns of genetic...

In recent years, evidence has been found that plant-pollinator interactions are altered by land-use and that genetic diversity also plays a role. However, how land-use and genetic diversity influence plant–pollinator interactions, particularly in the Neotropics, where many endemic plants exist is still an open question. Cucurbita pepo is a monoecio...

Background Plants have evolved physical–chemical defense to prevent/diminish damage by their enemies. Chemical defense involves the synthesis’ pathways of specialized toxic, repellent, or anti-nutritive metabolites to herbivores. Molecular evolutionary studies have revealed the origin of new genes, acquisition and functional diversification along t...

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...

Plant mating system determines, to a great extent, the demographic and genetic properties of populations, hence their potential for adaptive evolution. Variation in plant mating system has been documented between phylogenetically related species as well between populations of a species. A common evolutionary transition, from outcrossing to selfing,...

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...

We found interaction of seminatural areas and genetic diversity affecting nestedness. greater genetic diversity increased nestedness, but lower genetic diversity decreased nestedness even if seminatural areas were greater

Since most species are collections of genetically variable populations distributed to habitats differing in their abiotic/biotic environmental factors and community composition, the pattern and strength of natural selection imposed by species on each others' traits are also expected to be highly spatially variable. Here, we used genomic and quantit...

Natural enemy release is one main historical event that promotes the evolution of alien-colonizing plants in a new range. During this process, it is expected that selection on characters that mediated the interaction between plants and their herbivores in the native range will change the average trait values in the new range and other correlated re...

The annual herb, Datura stramonium, is a member of the Solanaceae family. In this study, we report the chloroplast genomes of two Mexican plants of D. stramonium. Both chloroplast genomes of D. stramonium (GenBank accessions: MT610896 and MT610897) were assembled as a circular molecule. The genome size of both plants was similar (155,884 bp). The o...

The interaction between plants and their herbivores has spurred the evolution of multiple traits in the resource base – the host plants – as well as the evolution and diversification of different feeding habits of their consumers. This volume examines the extent to which these relationships have led to the microevolution of plant defence traits (i....

Plants are frequently attacked by herbivores and pathogens and have evolved constitutive and induced defences to prevent/diminish fitness costs. Here, we review recent progress in the study of the defence genes in plants. The sophisticated signalling network of plant defence responses is elicited and driven by both herbivore-induced factors (e.g. e...

The annual herb, Datura stramonium, is a member of the Solanaceae family. In this study, we reported two chloroplast and mitochondrial genomes of two Mexican plants of Datura stramonium. Both chloroplast genomes contained 87 protein-coding genes, 157 genes, 7 rRNA genes and 62 tRNA genes. Both chloroplast genomes of D. stramonium had the same genom...

It is thought that natural selection exerted by herbivores on plants has promoted the evolution of plant traits that function as defence. However, such selective pressures may vary spatially differentiating populations in plant defence phenotypes. Yet, to ascertain the role of natural selection on phenotypic differentiation between populations, it...

Plant-herbivore interactions are a central topic in evolutionary ecology. Historically, their study has been a cornerstone for coevolutionary theory. Starting from classic ecological studies at the phenotypic level, it has since expanded to molecular and genomic approaches. After a historical perspective, the book’s subsequent chapters cover a wide...

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...

Theories of plant invasion based on enemy release in a new range assume that selection exerted by specialist herbivores on defence traits should be reduced, absent, or even selected against in the new environment. Here, we measured phenotypic selection on atropine and scopolamine concentration of Datura stramonium in eight native (Mexico) and 14 no...

Introduction Defoliation and light competition are ubiquitous stressors that can strongly limit plant performance. Tolerance to defoliation is often associated with compensatory growth, which could be positively or negatively related to plant growth. Genetic variation in growth, tolerance and compensation, in turn, plays an important role in the ev...

Allometric model. Details on methods of the construction of an allometric model for estimation of biomass per plant part of seedlings of 6 months of age. (DOCX)

Iterative growth model. Details on methods of the construction and adaptation of an iterative growth model for estimation of daily individual seedling NAR, flam and γ. (DOCX)

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...

Defoliation is a ubiquitous stressor that can strongly limit plant performance. Tolerance to defoliation is often associated with compensatory growth. Genetic variation in tolerance and compensatory growth responses, in turn, play an important role in the evolutionary adaptation of plants to changing disturbance regimes but this issue has been poor...

Article impact statement: Genomic information can help prevent species loss, facilitate reserve design and maximize adaptive potential of natural mangrove populations.

RESUMEN El conocimiento de las causas y mecanismos subyacentes de la plasticidad fenotípica en respuesta a la variación ambiental es crucial para un mejor entendimiento de la evolución y de la biodiversidad. En este trabajo se describe y analiza la importancia del estudio de la plasticidad fenotípica en plantas, mediante los trabajos de los últimos...

Little is known regarding the effect of fragmentation and human agricultural management on the genetic variation and gene flow of Cucurbita pepo L., 1753 in moderate fragmented areas in central Guatemala. We hypothesize that the genetic variation of C. pepo is affected by forest fragmentation and by traditional agricultural management. Therefore, w...

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...

A wealth of plant species used by humans for different purposes, but mainly as food, originated and domesticated in the Mesoamerican region. Papaya (Carica papaya) is the third most cultivated tropical crop worldwide, and it has been hypothesized that Mesoamerica is the most likely center of its origin and domestication. In support of it, many wild...

Plant populations invading new environments might compromise their fitness contribution to the next generation, because of the lack of native specialist pollinators and/or potential mates. Thus, changes in plant mating system and traits linked to it are expected in populations colonising new environments where selection would favour selfing and flo...

In the last century, Darwin and Haeckel were the first to propose the phylogenetic trees. The first phylogenies were made intuitively, but in the fifties several researchers tried to propose rules for their reconstruction. The evolutionary school in tended to use the principies of evolution, the numerical (or pheneticist) school advanced the "dista...

20 Question: Does light limitation reduce tolerance to leaf damage in the annual herb Datura 21 stramonium? 22 Hypothesis: Tolerance to leaf damage should be lower under light limitation (shade) than 23 under full sunlight, because a reduction in leaf area and lower exposure to light will limit 24 carbon photo-assimilation and plants' ability to ma...

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plan...

Mean geographic distance (km, in lower diagonal) and conditional genetic distances (cGD, in upper diagonal) between populations of Aphelandra aurantiaca

Genetic structure for twelve populations of Aphelandra aurantiaca ilustrated by Structure K = 2 and K = 3 were detected by Evanno, Regnaut & Goudet (2005) method of optimal number of genetic clusters. Each bar represents an individual and its proportional memebership to clusters. Populations are ordered from small to large fragments.

Geographic coordinates for the studied populations of Aphelandra aurantiaca at Los Tuxtlas, Mexico

Tests of population bottleneck for Aphelandra aurantiaca in different fragment sizes. Tests were based on heterozygosity excess TPM: two-phase model of mutation; SMM: step-wise mutation model. *P < 0.05 indicates significance of Wilcoxon’s signed –rank test.

First-generation migrants of Aphelandra aurantiaca among fragment sizes identified by GeneClass2 analysis (p < 0.01) Footnote: Resident fragment refers to the fragment size an individual was found at, fragment source indicates the most likely origin. L was estimated as L= -LOG (Lhome), where L is the ratio of the likelihood computed from the popula...

Comparison of the possible demographic scenarios for Aphelandra aurantiaca using Principal component analysis in DIYABC Scenario 4 fits the observed data best.

Prior parameters distribution of Aphelandra aurantiaca used in DIYABC and posterior parameters estimated for Scenario 4

Membership probabilities of Aphelandra aurantiaca to their populations of sampling extracted from DAPC Bold numbers indicate membership probabilities for individuals in their home population.

Network analysis (A) Community detection on Aphelandra aurantiaca network with medium threshold (0.245), using Fast Greedy and geographic coordinates algorithm implemented in NetStruct. Each node represents an individual, with colors representing the three community assigned. (B) SAD Analysis for the network, show the distributions of the SA values...

Discriminant Analysis of Principal Components for all populations estimated in DAPC, 50 PCA axes and 11 DA axes were retained

Microsatellite data of mating system of Aphelandra aurantiaca

Microsatellite data of genetic structure of Aphelandra aurantica

To understand the geographic distributions of rhizobia that associated with widely distributed wild legumes, 66 nodules obtained from 41 individuals including three sea-dispersed legumes (Vigna marina, Vigna luteola, and Canavalia rosea) distributed across the tropical and subtropical coastal regions of the world were studied. Partial sequences of...

Seed germination and seedling survival are fundamental processes in the life cycle of Podostemaceae, the largest family of strictly aquatic angiosperms. However, few studies to date have addressed seed germination and seedling survival of Podostemaceae under natural conditions. To fill this gap, we performed a field experiment to study the seed ger...

Background and aims Few studies have evaluated the genetic structure and evolutionary history of wild varieties of important crop species. The wild papaya (Carica papaya) is a key element of early successional tropical and sub-tropical forests in Mexico, and constitutes the genetic reservoir for evolutionary potential of the species. In this study...

Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and non-governmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variation within and among populations can ha...

• Premise of the study: Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant. • Methods and Results: Fifty-six A. aureum individuals from three populations were sampled and genotyped to c...

Chamaedorea alternans is a palm species that has suffered from selective extraction, and habitat loss. We collected 11 populations from fragmented and conserved forest. We assess genetic variation of C. alternans, genetic exchange, differentiation, bottlenecks, effective population size and signals of natural selection. Genetic diversity was higher...

To cope with the limiting light conditions in the rain forest understory, many tropical tree species have evolved large seeds that provide the emerging seedlings with nutritional reserves. Habitat fragmentation might change the adaptive value of seed size by modifying the biotic and physical conditions of the forest understory. We experimentally as...

Plant resistance to herbivores involves physical and chemical plant traits that prevent or diminish damage by herbivores, and hence may promote coevolutionary arm-races between interacting species. Although Datura stramonium’s concentration of tropane alkaloids is under selection by leaf beetles, it is not known whether chemical defense reduces see...

Geographic location, sample size, environmental characteristics, and average value (S.E.) of infestation, fruit and seed production of 31 populations of Datura stramonium in central Mexico. The number of each population corresponds to a locality given in Fig. 1.

Average concentration (mg g−1) of alkaloid of leaves and seeds per population of Datura stramonium

Seed predation by Trichobaris soror on Datura stramonium Infestation of Trichobaris soror to plants of Datura stramonium from 31 populations of central Mexico S is the selection differential of plant fitness (seeds) in relation to the concentration of atropine or scopolamine of leaves and seeds. See Methods.

Background: Biotypes of Avena fatua resistant to ACCase-inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesized that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow, due to t...

Las especies del género Cucurbita son monoicas, por lo que requieren del servicio de polinización para la transferencia de gametos (polen) entre flores masculinas y femeninas y producir semillas (Robinson & Decker, 1997). Además, presentan varios atributos, considerados putativamente adaptaciones para la polinización por insectos (ej. granos de pol...

Can the genetic structure of a specialist weevil be explained by the geological history of their distribution zone? We analyze the genetic variation of the weevil Trichobaris soror, a specialist seed predator of Datura stramonium, in order to address this question. For the phylogeographic analysis we used the COI gene, and assessed species identity...