Conservation genomics of the wild pumpkin Cucurbita radicans in Central Mexico: The influence of a changing environment on the genetic diversity and differentiation of a rare species.

The genetic diversity found in natural populations is the result of the evolutionary forces in response to historical and contemporary factors. The environmental characteristics and geological history of Mexico promoted the evolution and diversification of plant species, including wild relatives of crops such as the wild pumpkins (Cucurbita). Wild pumpkin species are found in a variety of habitats, evidencing their capability to adapt to different environments. Despite the potential value of wild Cucurbita as a genetic reservoir for crops, there is a lack of studies on their genetic diversity. Cucurbita radicans is an endangered species threatened by habitat destruction leading to low densities in small and isolated populations. Here, we analyze Genotype by Sequencing genomic data of the wild pumpkin C. radicans to evaluate the influence of factors like isolation, demographic history, and the environment shaping the amount and distribution of its genetic variation. We analyzed 91 individuals from 14 localities along its reported distribution. We obtained 5,107 SNPs and found medium-high levels of genetic diversity and genetic structure distributed in four main geographic areas with different environmental conditions. Moreover, we found signals of demographic growth related to historical climatic shifts. Outlier loci analysis showed significant association with the environment, principally with precipitation variables. Also, the outlier loci displayed differential changes in their frequencies in response to future global climate change scenarios. Using the results of genetic structure, outlier loci and multivariate analyses of the environmental conditions, we propose priority localities for conservation that encompass most of the genetic diversity of C. radicans.

Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia.

PREMISE: The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS: Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS: Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS: The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.

Historical, temporal, and geographic dynamism of the interaction between Agave and Leptonycteris nectar-feeding bats.

PREMISE: The 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. METHODS: We 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, we analyzed the geographic correlation between 96 Agave spp. and two of the Mexican Tequila bats, genus Leptonycteris. RESULTS: We found that Leptonycteris spp. interact with different Agave spp. over their migratory routes. We propose an interaction refuge in Metztitlán and Tehuacán-Cuicatlán areas, where Agave- Leptonycteris interaction has probably remained active. During the nonmigratory season, both bat species consume nectar of almost the same Agave spp., suggesting the possibility of a diffuse coevolution among Agave and Leptonycteris bats. CONCLUSIONS: We propose that in the areas related to migratory bat movements, each bat species interacts with different Agave spp., whereas in the areas occupied by nonmigrant individuals, both bat species consume nectar of almost the same Agave taxa.

A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.

Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.

Metabolomic Diversity in Microbial Mats Under Different Environmental Conditions: A Tool to Test Microbial Ecosystem Chemical Change.

Microbial mats are microbial communities capable of recycling the essential elements of life and considered to be the oldest evidence of microbial communities on Earth. Due to their uniqueness and limited sampling material, analyzing their metabolomic profile in different seasons or conditions is challenging. In this study, microbial mats from a small pond in the Cuatro Cienegas Basin in Coahuila, Mexico, were collected in wet and dry seasons. In addition to these samples, mesocosm experiments from the wet samples were set. These mats are elastic and rise after heavy rainfall by forming gas domes structures known as "Archean domes", by the outgassing of methanogenic bacteria, archaea, and sulfur bacteria. Extracts from all mats and mesocosms were subjected to untargeted mass spectrometry-based metabolomics and molecular networking analysis. Interestingly, each mat showed high chemical diversity that may be explained by the temporal dynamic processes in which they were sampled.

Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico.

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, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.

Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico.

PREMISE: Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. METHODS: We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. RESULTS: Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. CONCLUSIONS: Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.

Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude.

In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.

Non-adaptive evolutionary processes governed the diversification of a temperate conifer lineage after its migration into the tropics.

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 80 K 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.

Evolutionary ecology of Agave: distribution patterns, phylogeny, and coevolution (an homage to Howard S. Gentry).

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.

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

BACKGROUND: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. RESULTS: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. CONCLUSIONS: Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays.

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 shifts. RESULTS: We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity HE = 0.3646-0.7699; Z. mays subsp. mexicana HE = 0.5885-0.7671). We detected significant genetic structure among populations (DEST = 0.4332) with significant heterozygote deficiency (FIS = 0.1796), and variable selfing rates (sg2 = 0.0-0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity. CONCLUSIONS: Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations.

Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient.

PREMISE: Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. METHODS: We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. RESULTS: Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans-Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well-differentiated group. CONCLUSIONS: Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.

Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita.

Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.

Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize.

Climate change is one of the most important threats to biodiversity and crop sustainability. The impact of climate change is often evaluated on the basis of expected changes in species' geographical distributions. Genomic diversity, local adaptation, and migration are seldom integrated into future species projections. Here, we examine how climate change will impact populations of two wild relatives of maize, the teosintes Zea mays ssp. mexicana and Z. mays ssp. parviglumis. Despite high levels of genetic diversity within populations and widespread future habitat suitability, we predict that climate change will alter patterns of local adaptation and decrease migration probabilities in more than two-thirds of present-day teosinte populations. These alterations are geographically heterogeneous and suggest that the possible impacts of climate change will vary considerably among populations. The population-specific effects of climate change are also evident in maize landraces, suggesting that climate change may result in maize landraces becoming maladapted to the climates in which they are currently cultivated. The predicted alterations to habitat distribution, migration potential, and patterns of local adaptation in wild and cultivated maize raise a red flag for the future of populations. The heterogeneous nature of predicted populations' responses underscores that the selective impact of climate change may vary among populations and that this is affected by different processes, including past adaptation.

Tracing back the origin of pumpkins (Cucurbita pepo ssp. pepo L.) in Mexico.

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.

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana).

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.

Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts.

Arid biomes are particularly prominent in the Neotropics providing some of its most emblematic landscapes and a substantial part of its species diversity. To understand some of the evolutionary processes underlying the speciation of lineages in the Mexican Deserts, the diversification of Fouquieria is investigated, which includes eleven species, all endemic to the warm deserts and dry subtropical regions of North America. Using a phylogeny from plastid DNA sequences with samples of individuals from populations of all the species recognized in Fouquieria, we estimate divergence times, test for temporal diversification heterogeneity, test for geographical structure, and conduct ancestral area reconstruction. Fouquieria is an ancient lineage that diverged from Polemoniaceae ca. 75.54 Ma. A Mio-Pliocene diversification of Fouquieria with vicariance, associated with Neogene orogenesis underlying the early development of regional deserts is strongly supported. Test for temporal diversification heterogeneity indicates that during its evolutionary history, Fouquieria had a drastic diversification rate shift at ca.12.72 Ma, agreeing with hypotheses that some of the lineages in North American deserts diversified as early as the late Miocene to Pliocene, and not during the Pleistocene. Long-term diversification dynamics analyses suggest that extinction also played a significant role in Fouquieria's evolution, with a very high rate at the onset of the process. From the late Miocene onwards, Fouquieria underwent substantial diversification change, involving high speciation decreasing to the present and negligible extinction, which is congruent with its scant fossil record during this period. Geographic phylogenetic structure and the pattern of most sister species inhabiting different desert nucleus support that isolation by distance could be the main driver of speciation.

Historical biogeography and phylogeny of Cucurbita: Insights from ancestral area reconstruction and niche evolution.

Knowledge of the role of geographical and ecological events associated to the divergence process of wild progenitors is important to understand the process of domestication. We analysed the temporal, spatial and ecological patterns of the diversification of Cucurbita, an American genus of worldwide economic importance. We conducted a phylogenetic analysis based on six chloroplast regions (5907 bp) to estimate diversification rates and dates of divergence between taxa. This is the first phylogenetic study to include C. radicans, a wild species that is endemic to the Trans Mexican Volcanic Belt. We performed analysis of ancestral area reconstruction and paleoreconstructions of species distribution models to understand shifts in wild species ranges. We used principal component analysis (PCA) and multivariate analysis of variance (MANOVA) to evaluate the environmental differentiation among taxa within each clade. The phylogenetic analyses showed good support for at least six independent domestication events in Cucurbita. The genus Cucurbita showed a time of divergence of 11.24 Ma (6.88-17 Ma 95% HDP), and the dates of divergence between taxa within each group ranged from 0.35 to 6.58 Ma, being the divergence between C. lundelliana and C. okeechobeensis subsp. martinezii the most recent. The diversification rate of the genus was constant through time. The diversification of most wild taxa occurred during the Pleistocene, and its date of divergence is concordant with the dates of divergence reported for specialized bees of the genera Xenoglossa and Peponapis, suggesting a process of coevolution between Cucurbita and their main pollinators that should be further investigated. Tests of environmental differentiation together with ancestral area reconstruction and species distribution models past projections suggest that divergence was promoted by the onset of geographic barriers and secondary range contraction and by expansion related to glacial-interglacial cycles.