Erika Aguirre Planter - Academia.edu (original) (raw)

Books by Erika Aguirre Planter

Capítulo de libro sobre Diferenciación Genética.

Papers by Erika Aguirre Planter

bioRxiv (Cold Spring Harbor Laboratory), Apr 13, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

American Journal of Botany

PremiseThe interaction between ecological and evolutionary processes has been recognized as an im... more PremiseThe interaction between ecological and evolutionary processes has been recognized as an important factor shaping the evolutionary history of species. Some authors have proposed different ecological and evolutionary hypotheses concerning the relationships between plants and their pollinators; a special case is the interaction and suspected coevolution among Agave spp. and their main pollinators, the Leptonycteris bats. Agave spp. have, in general, a pollination syndrome compatible with chiropterophily including floral shape and size, nocturnal nectar production, and nectar quality and sugar concentration. Our goal was to analyze the interaction Agave–Leptonycteris and its dynamics during three different climate scenarios.MethodsWe modeled the Agave–Leptonycteris interaction in its spatial and temporal components during the Pleistocene using Ecological Niche Models (ENMs) and three climate scenarios: Current, Last Glacial Maximum (LGM), and Last InterGlacial (LIG). Furthermore,...

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...

Molecular Ecology

Secondary contact of recently diverged species may have several outcomes, ranging from rampant hy... more Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii–A. religiosa) distributed in “sky‐islands” across central Mexico (i.e., along the Trans‐Mexican Volcanic Belt; TMVB). Despite co‐occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, genera...

American Journal of Botany

With more than 200 species, the genus Agave is one of the most interesting and complex groups of ... more With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management.

Due to the recent increase in demand for agave-based beverages, many wild agave populations have ... more Due to the recent increase in demand for agave-based beverages, many wild agave populations have experienced rapid decline and fragmentation; whereas cultivated plants are now managed at monocultural plantations, in some cases involving clonal propagation. We examined the relative effect of migration, genetic drift, natural selection and human activities on the genetic repertoire of Agave angustifolia var. pacifica, an agave used for bacanora (an alcoholic spirit similar to tequila) production in northwestern Mexico. We sampled 34 wild and cultivated sites and used over eleven thousand genome-wide SNPs. We found shallow genetic structure among wild samples, although, detected differentiation between coastal and inland sites. Surprisingly, no differentiation was found between cultivated and wild populations. Moreover, we detected moderate inbreeding (FIS ∼ 0.13) and similar levels of genomic diversity in wild and cultivated agaves. Nevertheless, the cultivated plants had almost no pr...

Chromosome-level genome assemblies of Cucurbita argyrosperma subsp. a... more Chromosome-level genome assemblies of Cucurbita argyrosperma subsp. argyrosperma and Cucurbita argyrosperma subsp. sororia. These results are published in the paper "The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative" in Horticulture Research. Each genome contains the following files: - Genome_sequences -> Genome sequences in FASTA format of the nuclear genome (20 chromosomes + unscaffolded contigs), the mitochondrial genomes (fragmented) and the chloroplast genomes (complete circularized). - Gene_annotation -> Gene models predicted within the nuclear genomes in GFF3 format. - Gene_sequences -> FASTA sequences of the predicted gene models, including the amino acid sequences and the CDSs of the protein-coding genes, as well as the lincRNA transcripts in the case of C. argyrosperma subsp...

Supplemetary tables and figures cited in main manuscript

Supplementary methods for data analysis

a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity ... more a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean Ho ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (u 5 Fst ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (Fis ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions an...

Cucurbita pepo is an economically important crop, which consists of cultivated... more Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo's ancestor through Approximate Bayesian Computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo's ancestor.

bioRxiv, 2020

Despite their economic importance and well-characterized domestication syndrome, the genomic impa... more Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first wild Cucurbita genome at a chromosome level. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results ind...

Secondary contact of species that have evolved partial reproductive isolation in allopatry may re... more Secondary contact of species that have evolved partial reproductive isolation in allopatry may result in several outcomes, which range from rampant hybridization to barrier reinforcement. Reinforcement arises from reduced hybrid fitness, which promotes assortative mating and hence speciation. In plants, self-fertilization and disjunctions in reproductive-phenology are often invoked as evidence of reinforcement. However, local adaptation and pleiotropic effects during colonization can also lead to reproductive isolation without reinforcement. We explored these possibilities in a fir species complex (Abies flinckii - A. religiosa) distributed in ‘sky-islands’ along the Trans-Mexican Volcanic Belt (TMVB), in central Mexico. Despite co-occurring in two independent sympatric regions (west and center), these two taxa seem to rarely interbreed because of disjunct reproductive phenologies. We genotyped 1,147 SNPs, generated by GBS across 23 populations, and compared multiple demographic sce...

American journal of botany, 2020

PREMISE Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of ... more PREMISE Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers. METHODS We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent-based demographic analysis and species distribution modeling to evaluate the effects of historical environmental s...

Gene flow among crops and their wild relatives is an active study area in evolutionary biology an... more Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the t...

Plant Diversity and Ecology in the Chihuahuan Desert, 2020

The Chihuahuan desert is the largest and most diverse arid desert in North America. Geological an... more The Chihuahuan desert is the largest and most diverse arid desert in North America. Geological and climatic events of the Miocene–Pliocene, as well as the climatic cyclical changes of the Pleistocene, had an important effect on the diversity patterns of the species in this desert. Several areas of the Chihuahuan desert have been identified as “refuges” in which the arid biota survived or thrived during the complex Pleistocene climate changes, including Cuatro Cienegas, and Mapimian valleys, among other areas. We analyzed bibliographic genetic structure information from plant and animal species of the Chihuahuan desert, using the data to explore for general phylogeographic patterns. Our hypothesis was that the recent history of the genetic diversity currently observed could be interpreted in terms of the effects of large-scale geological and climatic events that occurred during Miocene/Pliocene. We analyzed 24 studies, 9 involving plants (Agave lechuguilla, A. striata, A. stricta, A. victoria-reginae, Astrophytum spp., Berberis trifoliate, Ephedra compacta, Leucophyllum spp., Larrea tridentata), and the rest involving animals. We detected three main patterns: (1) An ancient differentiation of the North of the Chihuahuan desert in the Cochise filter barrier area, within the Late Miocene (~11.6–5.3 MY), supported by three species; (2) A North/South differentiation from the Chihuahuan desert into the Altiplano Norte and Altiplano Sur, broadly congruent with the Pliocene (~5.3–2.5 MY) supported by seven species; (3) A divergence congruent with the Pleistocene (~2.5 MY), involving recent events within lineages. Another commonly detected pattern is an East/West differentiation. The current genetic differentiation patterns of the Chihuahuan desert species can be explained, at least in part, in terms of Pleistocene climate dynamics along an altitudinal and latitudinal gradient of locally adapted populations that underwent cyclic processes of contraction, isolation, and divergence, followed by expansion and secondary contact.

bioRxiv (Cold Spring Harbor Laboratory), Apr 13, 2022

American Journal of Botany

PeerJ

Molecular Ecology

American Journal of Botany

Supplemetary tables and figures cited in main manuscript

Supplementary methods for data analysis

bioRxiv, 2020

American journal of botany, 2020

Plant Diversity and Ecology in the Chihuahuan Desert, 2020

Molecular Phylogenetics and Evolution, 2021

Constructing phylogenetic relationships among closely related species is a recurrent challenge in... more Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of πa/πs and Ka/Ks with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics.