Biology subjects

Eguiarte, L. E.

Publications and source records attributed to Eguiarte, L. E..

At least 19 recordsLinked to original sources

bioRxiv2025

The Hidden Guardians: From Active Cells to Spores in a 20-Year Journey into the Microbial Heart of a Drying Oasis

The Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, a Ramsar Wetland, is historically characterized by a unique network of pozas renowned for microbial diversity. Among them, the Churince hydrological system epitomized a delicate balance of endemic species, stable water regimes, and complex microbial assemblages. Over the last five decades, however, Churince underwent a catastrophic [~]99% water loss, primarily driven by intensive agricultural extraction. We showed that this desiccation not only caused hydrological collapse but also reshaped microbial physiology. Longitudinal records from 2007 to 2019, combining satellite imagery, piezometer data, and field observations, documented progressive declines beginning in 2011 and culminating in the complete desiccation of the Intermediate Lagoon by 2019. To track microbial responses, we employed a cultivation-based approach distinguishing vegetative cells from dormant spores, enabling direct physiological assessment of metabolic activity versus dormancy. As water diminished, spore abundance increased relative to vegetative forms, revealing a shift toward dormancy as a survival strategy under extreme desiccation. Complementary mesocosm experiments showed that reduced diversity further enriched for spores, illustrating how loss of community complexity accelerated dormancy and erosion of active assemblages. Together, these results demonstrated that habitat loss triggered microbial community change, which we frame as a microbial extension of the ecological concept of community disassembly. By combining two decades of hydrological evidence with microbial physiology, this study fills a critical gap in understanding how wetland drying selects for microbial dormancy. These findings underscore the urgent need for sustainable agriculture and integrated water management to preserve biodiversity and ecosystem function in threatened wetlands worldwide.

microbiology↗

bioRxiv2025

How social and economic policies have affected the genome of mezcal agaves: the contrasting stories of Bacanora and Espadin

Plant domestication in Mesoamerica gave the world crops of global significance, such as maize, beans, squashes, cocoa, and cotton. Additionally, it has introduced species of regional economic importance, which still display intermediate levels of domestication, including Agave, Opuntia, columnar cacti, Amaranthus, and various ornamental species. Agaves, in particular, hold immense cultural and economic significance in Mexico and play a crucial ecological role in wild plant communities. However, current agricultural practices have negatively impacted both wild populations of agave through overexploitation and habitat destruction, as well as cultivated plants by reducing available landraces and promoting the use of homogeneous plant material. Using genomic data (RADseq) and over 50,000 SNPs, we aimed to assess how local social and political decisions may have influenced genomic diversity and differentiation in intensively managed, clonally propagated Agave angustifolia (Espadin) in the state of Oaxaca, as well as in the cultivated A. angustifolia used to produce mezcal known as Bacanora in the state of Sonora and their wild counterparts from both regions. We found evidence suggesting that Espadin recently aroused through farmer selection of a clonal lineage with desirable mezcal production attributes (i.e., hybrid vigor), apparently from a cross between genetically distinct wild populations or by hybridization between wild and cultivated varieties. Espadin samples were represented by closely related heterozygous genotypes, with considerable genetic differentiation from wild plants. On the other hand, the genomic composition of cultivated Bacanora agave apparently was influenced by a recently lifted ban (in 1992) on its cultivation and distillation, which, along with the relatively lower popularity of this beverage, allowed cultivated Bacanora agave to maintain the genetic diversity found in wild populations of the regions. We found that social and political decisions may have important impacts on crop genomic diversity and differentiation.

plant biology↗

bioRxiv2024

Running against the clock: describing microbial diversity in an extremely endangered microbial oasis in the Chihuahuan desert

Cuatro cienegas Basin (CCB) is an extraordinary diverse oasis that is dying in front of our eyes. The Churince system disappeared completely in 2016 and the poza named for its amazing diversity, Archaean Domes, disappeared in 2023. However, there could be groundwater water connections between sites, allowing to dispersal of taxa as well as the survival of microbial lineages in the deep aquifer Herein, we explore whether there is microbial connectivity across sites in the oasis of CCB, located in the Chihuahuan Desert, in the Northern state of Coahuila in Mexico. We focused first on two distinct aquatic system within CCB that are [~]4700 meters apart on the Eastern lobe of the basin: Pozas Rojas -a preserved system characterized by several unique ponds surrounding a deep lagoon, and the now extinct Archean Domes (AD)--noted for its extreme salinity, as well as anoxic and methane-rich conditions. We sequenced the hypervariable V4 region of the 16S rRNA gene from samples of Pozas Rojas (PR), and of two different features in AD: orange circles (C) and dome-shaped structures (D). Additionally, we utilized whole-genome metagenomic data from different samples from AD site (from the years 2016 to 2023). Second, we compared metagenomes obtained from the now extinct Churince (samples from 2012 to 2014) in the West lobe of the basin, with the Easter side. Our results revealed taxa common to different sites, including Halanaerobium sp. and Desulfovermiculus sp., that are prevalent across samples from PR and AD, and shared between AD and Churince, suggesting that those genera are core to the deep aquifer. Moreover, during the eight years of sampling, AD exhibited a substantial decline in microbial diversity. Possibly, this decline, as well as Churince demise, is due to anthropogenic disturbances of the deep aquifer due to overexploitation for alfalfa irrigation. Diversity in metagenome-assembled genomes (MAGs) decreasing from 125 MAGs in 2016 to only 22 in 2023. Our study supports the hypothesis of the importance of groundwater as a fundamental microbial reservoir and connector among CCB ponds. Therefore, the regulation of extraction of such aquifer is paramount.

microbiology↗

bioRxiv2023

Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico

The sheer diversity of unculturable viruses has prompted the need to describe new viruses through culture-independent techniques. The associated host is one important phenotypic feature that can be inferred from metagenomic viral contigs -- thanks to the development of various bioinformatic tools. Here we compare the performance of recently developed tools for virus-host prediction on a dataset of 1,046 virus-host pairs and then apply the best-performing tools on a metagenomic dataset derived from a highly diverse transiently hypersaline site known as Archaean Domes within the Cuatro Cienegas Basin, Coahuila, Mexico. We also introduce a virus-host prediction tool called CrisprCustomDB, which uses specific criteria to solve controversial host assignments with custom spacers databases. Host-dependent alignment-based methods showed an average precision of 83% and a sensitivity from 13.7% to 17.7%, whereas host-dependent alignment-free methods achieved an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best performance overall (F1_score = 95.7%). However, when applied to the highly diverse metagenomic dataset, the host-dependent alignment-based (e.g., CrisprCustomDB) and alignment-free (e.g., PHP) methods showed the greatest agreement with each other, even though they are fundamentally different methods. This is because instead of depending on known hosts or viruses-with-known-host databases, they can directly relate metagenomic viral contigs and metagenome-assembled genomes from the same dataset. Such methods also showed the greatest consistency between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism, revealing that Archaean Domes viruses likely infect halophilic Archaea as well as a variety of Bacteria which may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing or marine-related. Consequently, using a combination of methods and qualitative validations relating to the source environment and the predicted host biology will increase the number of correct predictions, mainly when dealing with novel viruses.

bioinformatics↗

bioRxiv2023

Unveiling Local Radiation Events through Metagenome Assembled Genomes of Archaea and Bacteria in Hypersaline Microbial Mats from the Archean Domes Site, Cuatro Cienegas, Coahuila, Mexico

A comprehensive study was conducted in the Cuatro Cienegas Basin (CCB) in Coahuila, Mexico, known for its remarkable microbiological diversity and unique physicochemical properties. The ''Archaean Domes '' (DA) in the CCB are hypersaline, non-lithifying microbial mats. This study focused on analyzing the small domes and circular structures formed in DA through metagenome assembly genomes (MAGs) with the aim of finding new microorganisms and providing information on the tree of life in a place as diverse as the CCB. In total, 329 MAGs were identified, including 52 archaea and 277 bacteria. Remarkably, 30 Archaea and 154 Bacteria could not be classified at the genus level, highlighting the remarkable diversity of CCB. The CCBs showed significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Euryarchaeota, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, Chloroflexi, Planctomycetes, Candidatus Parvarchaeota, Verrucomicrobia, Balneolaeota, Nitrospirae, and Tenericutes. Subsequently, the MAGs were classified into a phylogenetic tree. In Archaea, monophyletic groups MAGs belonged to the phyla Archaeoglobi, Candidatus Aenigmarchaeota, Candidatus Nanoarchaeota, Candidatus Lokiarchaeota, and Halobacteriota. Among the Bacteria, monophyletic groups were identified as well, including Spirochaetes, Proteobacteria, Planctomycetota, Actinobacteria, Verrucomicrobiota, Bacteroidetes, Bipolaricaulota, Desulfobacterota, and Cyanobacteria. These monophyletic clusters may indicate radiation events that are likely influenced by geographical isolation as well as extreme environmental conditions reported in AD pond like phosphorus deficiency (122:42:1 C:N:P), fluctuating pH and a salinity of 5.28%

microbiology↗

bioRxiv2023

Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus

Genetic differentiations and phylogeographical patterns are controlled by the interplay between spatial isolation and gene flow. To test the extent of gene flow across an oceanic barrier, we explored the effect of the separation of the peninsula of Baja California on the evolution of mainland and peninsular populations of the long-lived columnar cactus Stenocereus thurberi. We analyzed twelve populations throughout the OPC distribution range to assess genetic diversity and structure using chloroplast DNA sequences. Genetic diversity was higher (Hd=0.81), and genetic structure was lower (GST=0.143) in mainland populations vs peninsular populations (Hd=0.71, GST=0.358 respectively). Genetic diversity was negatively associated with elevation but positively with rainfall. Two mainland and one peninsular ancestral haplotypes were reconstructed. Peninsular populations were as isolated among them as with mainland populations. Peninsular haplotypes formed a group with one mainland coastal population, and populations across the gulf shared common haplotypes giving support to regular gene flow across the Gulf. Gene flow is likely mediated by bats, the main pollinators and seed dispersers. Niche modeling suggests that during the Last Glacial Maximum (c. 130 ka), OPC populations shrank to southern locations. Currently, Stenocereus thurberi populations are expanding, and the species is under population divergence despite ongoing gene flow. Ancestral populations are located on the mainland and although vicariant peninsular populations cannot be ruled out, they are likely the result of gene flow across the seemingly formidable barrier of the Gulf of California. Still, unique haplotypes occur in the peninsula and the mainland, and peninsular populations are more structured than these on the mainland.

evolutionary biology↗

bioRxiv2022

Metagenomic insight into taxonomic composition, environmental filtering, and functional redundancy for shaping worldwide modern microbial mats

Although microbial mats are considered relictual communities that are nowadays mostly constrained in their distribution by predation and phosphorus availability, they are still found in a wide range of environmental conditions. Their ancestral history, geographical isolation, stratified community composition and interspecies dynamics make them an interesting model to study community ecological processes and concepts. In this study, we analyzed different metagenomic datasets from worldwide modern microbial mats to compare community structure and functions. We found significant differentiation in both alpha and beta diversity of taxonomic and functional categories without significant correlation with temperature and pH. Differences depended more on the presence of very highly abundant cyanobacteria and some generalist microorganisms. Our results suggest that there is more than just Grinnellian niche dynamics in the determination of microbial mat community assembly, opening the hypothesis of interactions as the driver behind these ancient communities. We also discuss the influence of niche dynamics and environmental filtering in the community assembly of microbial mats.

ecology↗

bioRxiv2022

Genomic analyses of wild and cultivated bacanora agave (Agave angustifolia var. pacifica) reveal inbreeding, few signs of cultivation history and shallow population structure

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 private alleles and presented evidence of clonality. The overall low genetic structure in A. angustifolia var. pacifica is apparently the result of high dispersibility promoted by pollinators and possibility of clonal reproduction. Incipient cultivation history and reliance on wild seeds and plants are probably responsible for the observed patterns of high genetic connectivity and considerable diversity in cultivated samples.

plant biology↗

bioRxiv2021

Strengthened mutualistic adaptation between teosinte and its rhizosphere biota in cold climates

O_LIWhile abiotic environments consistently shape local adaptation, the strength of local adaptation to biotic interactions may vary more. One theory, COCO (CO-evolutionary Outcomes across Conditionality), predicts it may be strongest where species experience greater stress, because stress increases fitness impacts of species interactions. For example, in plant interactions with rhizosphere biota, positive outcomes increase with stress from low soil fertility, drought and cold. C_LIO_LITo investigate the influence of abiotic stress gradients on adaptation between plants and rhizosphere biota, we used a greenhouse common garden experiment recombining teosinte, Zea mays ssp. mexicana (wild relative of maize), and rhizosphere biota, collected across a stress gradient (elevational variation in temperature, precipitation, and nutrients). C_LIO_LIWe found stronger local adaptation between teosinte and rhizosphere biota from colder, more stressful sites, as expected by COCO. However, biota from less stressful, warmer sites provided greater average benefits across teosinte populations. Links between plant traits and 20-element profiles of plant leaves explained fitness variation, persisted in the field, were influenced by both plants and biota, and largely reflected patterns of local adaptation. C_LIO_LIIn sum, we uncovered greater local adaptation to biotic interactions in colder sites, and that both plants and rhizosphere biota affect the expression of plant phenotypes. C_LI

evolutionary biology↗

bioRxiv2021

Ecological relevance of abundant and rare taxa in a high-diverse elastic hypersaline microbial mat, using a small-scale sampling

We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Cienegas Basin (CCB) in the Chihuahuan Desert of Coahuila, Mexico. We collected ten samples on a small scale transect (1.5-meters) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faiths Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.

microbiology↗

bioRxiv2020

A wild Cucurbita genome reveals the role of structural variants and introgression in domestication

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 indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We uncovered candidate domestication genes that are involved in the synthesis and regulation of growth hormones, plant defense mechanisms, flowering time and seed development. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

evolutionary biology↗

bioRxiv2020

Evidence of anthropogenic perturbation in the genomic evolution of an environmental strain of Pseudomonas otitidis from Cuatro Cienegas, Coahuila, Mexico

Anthropogenic perturbations such as water overexploitation introduce novel selective pressures to the natural environments, impacting on the genomic variability of organisms and thus altering the evolutionary trajectory of its populations. Bad agricultural practices and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction together with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis, inhabitant to a particularly affected lagoon of an exhaustively studied system in the middle of the desert, over a 13 year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response of this bacterial lineage to the perturbation. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which, alongside an increment in mean Tajimas D and recombination rate, loss of genetic and nucleotidic variation and a single amino acid under positive selection, points the occurrence of an evolutionary rescue event, possibly potentiated by horizontal gene transfer, where the population nearly went extinct during the first desiccation event but sharply recovered in the second and adapted to its new environment. Furthermore, the gain of phosphorylation, DNA recombination and small-molecule metabolism and loss of biosynthetic and regulation genes on the exclusive accessory genome suggest a functional shift to a more generalist scavenger lifestyle in an environment that went from oligotrophic to nutrient-rich.

evolutionary biology↗

bioRxiv2020

Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize.

Massive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

genomics↗

bioRxiv2019

The role of historical and contemporary environmental factors in the distribution of genetic diversity in the teosinte in Mexico

Wild maize, commonly known as teosinte, has a wide distribution in central Mexico and inhabits a wide range of environmental conditions. According to previous studies, the environment is a determinant factor for the amount and distribution of genetic diversity. In this study, we used a set of neutral markers to explore the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods. Using a set of 22 nuclear microsatellite loci, we genotyped 527 individuals from 29 localities. We found highly variable levels of genetic diversity (Z. m. parviglumis HE= 0.3646-0.7699; Z. m. mexicana HE= 0.5885-0.7671) and significant genetic structure among localities (average DEST= 0.4332). Also, we recovered significant values of heterozygote deficiency (average FIS= 0.1796) and variable levels of selfing (sg2=0.0-0.3090). The Bayesian assignment analysis yielded four genetic clusters dividing the sample into subspecies, that in turn, were separated into two clusters. Environmental conditions played a strong influence in the distribution of genetic diversity, as demographic analysis and changes in species range revealed by modeling analyses were consistent. We conclude that current genetic diversity in teosinte is the result of a mixture of local adaptation and genetic isolation along with historical environmental fluctuations.

evolutionary biology↗

bioRxiv2019

Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

evolutionary biology↗

bioRxiv2019

Diversity of Archaea Domain in Cuatro Cienegas Basin: Archaean Domes.

Herein we describe the Archaea diversity in a shallow pond in the Cuatro Cienegas Basin (CCB), Northeast Mexico, with fluctuating hypersaline conditions containing elastic microbial mats that can form small domes where their anoxic inside reminds us of the characteristics of the Archaean Eon, rich in methane and sulfur gases; thus, we named this site the Archaean Domes (AD). These domes only form after heavy rains that are rare in the Chihuahuan desert. CCB is a unique oasis with hundreds of ponds, containing endemic species of animals, plants and highly diverse and unique microbial communities, despite its very biased stoichiometry, due mostly to extreme low phosphorus content (soils, water columns and sediments). This extreme oligotrophy has favored survival of ancestral microorganisms. Whole metagenome sequencing approach was performed for this unusual site in three different seasons to assess the extent of the Archaea biodiversity, with a focus on extremophiles, since members of the Archaea had been underrepresented in different study sites within the oasis. We found a highly diverse Archaea community compassing [~]5% of the metagenomes. The archaeal portion in all three metagenomes maintained its abundance and most of the strains showed to form a resilient core during three seasonal samplings (2016-2017), despite environmental fluctuations. However, relative abundances of all 230 archaeal OTUs (defined using a 97% cutoff) were low enough (<0.1%) to be considered part of the rare biosphere. AD finding and their description within CCB confirms that this particular pond is the most diverse for Archaea that we are aware of and opens new paths for understanding the forces that once drove and keep shaping microbial community assemblage.

microbiology↗

bioRxiv2019

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

Several universal genomic traits affect the capacity, cost, and efficiency of biochemical information processing underpinning metabolism and reproduction. We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Cienegas, Mexico--one of the first whole-ecosystem experiments involving replicated metagenomic assessments. As predicted assuming oligotrophy favors lower information-processing costs whereas copiotrophy favors higher processing rates, mean bacteria genome size was higher in the fertilized treatment, as were GC content, total number of tRNA genes, total number of rRNA genes and codon usage bias in ribosomal protein sequences. However, contrasting changes in trait variances also suggested differences between traits in mediating assembly under oligotrophic versus copiotrophic conditions. Tradeoffs in information-processing traits are apparently sufficiently pronounced to play a role in community assembly and all different components of metabolism-- information, energy, and nutrient requirements--are fine-tuned to an organisms growth and trophic strategy.

ecology↗

bioRxiv2019

Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes

Local adaptation across species range is widespread. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Because elevation gradients display continuous environmental changes at a short geographical scale, they provide an exceptional opportunity to investigate these questions. Here, we used two common gardens to phenotype 1664 plants from 11 populations of annual teosintes. These populations were sampled across two elevation gradients in Mexico. Our results point to a syndrome of adaptation to altitude with the production of offspring that flowered earlier, produced less tillers, and larger, longer and heavier grains with increasing elevation. We genotyped these plants for 178 outlier single nucleotide polymorphisms (SNPs), which had been chosen because they displayed excess of allele differentiation and/or correlation with environmental variables in six populations with contrasted altitudes. A high proportion of outlier SNPs associated with the phenotypic variation of at least one trait. We tested phenotypic pairwise correlations between traits, and found that the higher the correlation, the greater the number of common associated SNPs. In addition, allele frequencies at 87 of the outlier SNPs correlated with an environmental component best summarized by altitudinal variation on a broad sample of 28 populations. Chromosomal inversions were enriched for both phenotypically-associated and environmentally-correlated SNPs. Altogether, our results are consistent with the set-up of an altitudinal syndrome promoted by local adaptation of teosinte populations in the face of gene flow. We showed that pleiotropy is pervasive and potentially has constrained the evolution of traits. Finally, we recovered variants underlying phenotypic variation at adaptive traits. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding. Author summaryAcross their native range, species encounter a diversity of habitats promoting local adaptation of geographically distributed populations. While local adaptation is widespread, much has yet to be discovered about the conditions of its emergence, the targeted traits, their molecular determinants and the underlying ecological drivers. Here we employed a reverse ecology approach, combining phenotypes and genotypes, to mine the determinants of local adaptation of teosinte populations distributed along two steep altitudinal gradients in Mexico. Evaluation of 11 populations in two common gardens located at mid-elevation pointed to the set-up of an altitudinal syndrome, in spite of gene flow. We scanned genomes to identify loci with allele frequencies shifts along elevation. Interestingly, variation at these loci was commonly associated to variation of phenotypes. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding.

evolutionary biology↗