Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles †

Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra

Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia:Nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species

BACKGROUND: New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. RESULTS: The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. CONCLUSIONS: The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-014-0171-6) contains supplementary material, which is available to authorized users

Genómica de Poblaciones: Nada en Evolución va a tener sentido si no es a la luz de la Genómica, y nada en Genómica tendrá sentido si no es a la luz de la Evolución

The theory of population genetics originated over 80 years ago and allowed to explain, in terms of the evolutionary forces, the patterns of genetic variation within and between the populations that conform species. This research program generated the questions that have been empirically analyzed with the use of molecular markers for the last 50 years. A fundamental question within population genetics is if a reduced number of genes are representative of the evolutionary forces that affect the total genome of a species. This question has led to the development of molecular methods that allow the study of large sections of the genome in natural populations, giving rise to the field of population genomics. In recent years, techniques that are able to sequence DNA massively, usually called "Next generation sequencing" or "next-gen", are helping us to obtain genome wide data in many species, without needing previous molecular information. Comparing the genomes of many individuals from different populations, now we have access to an archive of their evolutionary history that narrates the complex and dynamic balance in time between natural selection and other evolutionary forces, such as genetic drift and gene flow, which act mainly in neutral regions of the genomes. The amount of information that is being produced has required the development of new statistical and bioinformatics tools for their analyses. Diverse disciplines have profited from these new developments. In particular in evolutionary biology it is now possible to study in a more precise way the adaptive patterns of variation. The annotation of genomes and the mapping of traits are important and complicated, but recent technical developments are making these goals easier, and thus the future challenge will be in asking the right questions to make relevant inferences from the sea of information these new methods generate. The evolutionary and population genetics perspective will enrich genomics, in the same way that the genomic data will help us advance in the development of the program initiated by Theodosius Dobzhansky several decades ago.La teoría de la genética de poblaciones surgió hace más de 80 años y nos permite explicar los patrones de variación genética dentro y entre las poblaciones que forman a las especies en términos de las fuerzas evolutivas. Este programa de investigación generó las preguntas que se han abordado empíricamente mediante marcadores moleculares desde hace medio siglo. Una pregunta fundamental ha sido hasta dónde un conjunto reducido de loci es o no representativo del efecto de las fuerzas evolutivas, sobre todo el genoma de una especie. Esto ha llevado al desarrollo creciente de aproximaciones que permitan conocer de manera representativa los niveles de variación genética en las poblaciones naturales, dando origen a la genómica de poblaciones. En años recientes, las técnicas de secuenciación masiva, llamadas Next generation sequencing, o next-gen, han permitido obtener datos de grandes secciones del genoma de diferentes especies, sin que sea un requisito conocer marcadores previos. Así, al comparar los genomas de muchos individuos de diferentes poblaciones, tenemos acceso al archivo de su historia evolutiva, que nos habla del complejo y dinámico balance en el tiempo entre la selección natural y las otras fuerzas evolutivas de carácter neutral, como la deriva y el flujo génico. La existencia de enormes cantidades de información ha requerido el desarrollo de nuevas herramientas estadísticas y bioinformáticas para su análisis. Diversas disciplinas se han visto beneficiadas de estos desarrollos. Para la biología evolutiva se abre la posibilidad de estudiar de manera más precisa y clara los patrones adaptativos de la variación. Tener genomas anotados y loci bien mapeados es relevante y arduo, pero el desarrollo técnico hace que lo anterior sea cada vez más plausible, y el reto será ser capaces de plantear preguntas adecuadas para hacer inferencias del mar de información disponible. El uso de una perspectiva evolutiva y de genética de poblaciones, enriquecerá a la genómica, de la misma manera que los datos genómicos nos ayudarán a avanzar en el desarrollo del programa iniciado por Theodosius Dobzhansky a mediados del siglo pasado

Genómica de poblaciones: nada en evolución va a tener sentido si no es a la luz de la genómica, y nada en genómica tendrá sentido si no es a la luz de la evolución

La teoría de la genética de poblaciones surgió hace más de 80 años y nos permite explicar los patrones de variación genética dentro y entre las poblaciones que forman a las especies en términos de las fuerzas evolutivas. Este programa de investigación generó las preguntas que se han abordado empíricamente mediante marcadores moleculares desde hace medio siglo. Una pregunta fundamental ha sido hasta dónde un conjunto reducido de loci es o no representativo del efecto de las fuerzas evolutivas, sobre todo el genoma de una especie. Esto ha llevado al desarrollo creciente de aproximaciones que permitan conocer de manera representativa los niveles de variación genética en las poblaciones naturales, dando origen a la genómica de poblaciones. En años recientes, las técnicas de secuenciación masiva, llamadas Next generation sequencing, o next-gen, han permitido obtener datos de grandes secciones del genoma de diferentes especies, sin que sea un requisito conocer marcadores previos. Así, al comparar los genomas de muchos individuos de diferentes poblaciones, tenemos acceso al archivo de su historia evolutiva, que nos habla del complejo y dinámico balance en el tiempo entre la selección natural y las otras fuerzas evolutivas de carácter neutral, como la deriva y el flujo génico. La existencia de enormes cantidades de información ha requerido el desarrollo de nuevas herramientas estadísticas y bioinformáticas para su análisis. Diversas disciplinas se han visto beneficiadas de estos desarrollos. Para la biología evolutiva se abre la posibilidad de estudiar de manera más precisa y clara los patrones adaptativos de la variación. Tener genomas anotados y loci bien mapeados es relevante y arduo, pero el desarrollo técnico hace que lo anterior sea cada vez más plausible, y el reto será ser capaces de plantear preguntas adecuadas para hacer inferencias del mar de información disponible. El uso de una perspectiva evolutiva y de genética de poblaciones, enriquecerá a la genómica, de la misma manera que los datos genómicos nos ayudarán a avanzar en el desarrollo del programa iniciado por Theodosius Dobzhansky a mediados del siglo pasado

Genomic Analyses of Wild and Cultivated Bacanora Agave (<i>Agave angustifolia</i> var. <i>pacifica</i>) 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 we 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 the 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

Uses, Knowledge and Extinction Risk Faced by <i>Agave</i> Species in Mexico

We compiled an updated database of all Agave species found in Mexico and analyzed it with specific criteria according to their biological parameters to evaluate the conservation and knowledge status of each species. Analyzing the present status of all Agave species not only provides crucial information for each species, but also helps determine which ones require special protection, especially those which are heavily used or cultivated for the production of distilled beverages. We conducted an extensive literature review search and compiled the conservation status of each species using mainstream criteria by IUCN. The information gaps in the database indicate a lack of knowledge and research regarding specific Agave species and it validates the need to conduct more studies on this genus. In total, 168 Agave species were included in our study, from which 89 are in the subgenus Agave and 79 in the subgenus Littaea. Agave lurida and A. nizandensis, in the subgenus Agave and Littaea, respectively, are severely endangered, due to their endemism, lack of knowledge about pollinators and floral visitors, and their endangered status according to the IUCN Red List. Some species are at risk due to the loss of genetic diversity resulting from production practices (i.e., Agave tequilana), and others because of excessive and unchecked overharvesting of wild plants, such as A. guadalajarana, A. victoriae-reginae, A. kristenii, and others. Given the huge economic and ecological importance of plants in the genus Agave, our review will be a milestone to ensure their future and continued provision of ecosystem services for humans, as well as encouraging further research in Agave species in an effort to enhance awareness of their conservation needs and sustainable use, and the implementation of eco-friendly practices in the species management

Population Genomics of Domesticated <i>Cucurbita ficifolia</i> Reveals a Recent Bottleneck and Low Gene Flow with Wild Relatives

Cucurbita ficifolia is a squash grown from Mexico to Bolivia. Its ancestor is unknown, but it has limited compatibility with wild xerophytic Cucurbita from Mexico’s highlands. We assembled the reference genome of C. ficifolia and assessed the genetic diversity and historical demography of the crop in Mexico with 2524 nuclear single nucleotide polymorphisms (SNPs). We also evaluated the gene flow between C. ficifolia and xerophytic taxa with 6292 nuclear and 440 plastome SNPs from 142 individuals sampled in 58 sites across their area of sympatry. Demographic modelling of C. ficifolia supports an eight-fold decrease in effective population size at about 2409 generations ago (95% CI = 464–12,393), whereas plastome SNPs support the expansion of maternal lineages ca. 1906–3635 years ago. Our results suggest a recent spread of C. ficifolia in Mexico, with high genetic diversity (π = 0.225, FST = 0.074) and inbreeding (FIS = 0.233). Coalescent models suggest low rates of gene flow with C. radicans and C. pedatifolia, whereas ABBA-BABA tests did not detect significant gene flow with wild taxa. Despite the ecogeographic proximity of C. ficifolia and its relatives, this crop persists as a highly isolated lineage of puzzling origin

Domesticación, diversidad y recursos genéticos y genómicos de México: El caso de las calabazas

The domestication of plants and animals allows the study of different evolutionary processes, including selection, adaptation and speciation. Here we describe recent advances in the study of pumpkins and squashes, which constitute the genus Cucurbita (Cucurbitaceae), being a group of herbaceous plants from the Americas that include between 12 and 15 species. Cucurbita has had six domestication events, four of them occurred in Mexico. This is a relatively recent genus that originated in North America 16 million years ago and its cultivated species maintain high levels of genetic variation. Cucurbita pepo is the species with the highest genetic diversity, diversity associated to two independent domestications, one in Northern Mexico and the other in Southern United States. In another species, Cucurbita argyrosperma, the populations from Yucatan Peninsula represents a genetic pool differentiated from the rest of the species. The study of the genome of C. argyrosperma and related taxa has revealed the regions of its genome associated with domestication. The populations of the species of this genus represent a source of important genetic resources in the face of climate change and constitute a good system for the study of domestication and of different evolutionary processes.La domesticación de plantas y animales permite estudiar diferentes procesos evolutivos, como la selección, adaptación y especiación. En este artículo se describen avances recientes en el estudio de las calabazas, las cuales constituyen el género Cucurbita (Cucurbitaceae) siendo un grupo de plantas herbáceas americanas que incluyen entre 12 y 15 especies. Cucurbita ha tenido seis eventos de domesticación, de los cuales cuatro sucedieron en México. Este es un género relativamente reciente, que surgió en Norte América hace 16 millones de años y sus especies cultivadas mantienen una alta variación genética; Cucurbita pepo es la especie que presenta mayor variación genética,variación asociada a dos domesticaciones independientes, una en el norte de México, y otra en el Sureste de los Estados Unidos. En otra especie, Cucurbita argyrosperma, sus poblaciones de la Península de Yucatán, representan una poza genética diferenciada del resto de la especie. El estudio del genoma de C. argyrosperma y taxa cercanos ha revelado las regiones de su genoma asociadas a la domesticación. Las poblaciones de las especies de este género representan una fuente de importantes recursos genéticos frente al cambio climático y constituyen un buen sistema para el estudio de la domesticación y de diferentes procesos evolutivos

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (&lt;0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene

Data_Sheet_1.PDF

<p>Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (H_E = 0.428 in sororia, and H_E = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (F_ST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.</p