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Macroevolutionary patterns in the association between plant species and their herbivores result from ecological divergence promoted by, among other factors, plants’ defenses and nutritional quality, and herbivore adaptations. Here, we assessed the performance of the herbivores Lema trilineata daturaphila, a trophic specialist on Datura, and Spodoptera frugiperda, a polyphagous pest herbivore, when fed with species of Datura. We used comparative phylogenetics and multivariate methods to examine the effects of Datura species’ tropane alkaloids, leaf trichomes, and plant macronutrients on the two herbivores´ performances (amount of food consumed, number of damaged leaves, larval biomass increment, and larval growth efficiency). The results indicate that species of Datura do vary in their general suitability as food host for the two herbivores. Overall, the specialist performs better than the generalist herbivore across Datura species, and performance of both herbivores is associated with suites of plant defenses and nutrient characteristics. Leaf trichomes and major alkaloids of the Datura species are strongly related to herbivores’ food consumption and biomass increase. Although hyoscyamine better predicts the key components of the performance of the specialist herbivore, scopolamine better predicts the performance of the generalist; however, only leaf trichomes are implicated in most performance components of the two herbivores. Nutrient quality more widely predicts the performance of the generalist herbivore. The contrasting effects of plant traits and the performances of herbivores could be related to adaptive differences to cope with plant toxins and achieve nutrient balance and evolutionary trade-offs and synergisms between plant traits to deal with a diverse community of herbivores.

In land plants, heteroblasty broadly refers to a drastic change in morphology during growth through ontogeny. Juniperus flaccida and Pinus cembroides are conifers of independent lineages known to exhibit leaf heteroblasty between the juvenile and adult life stage of development. Juvenile leaves of P. cembroides develop spirally on the main stem and appear decurrent, flattened and needle-like; whereas, adult photosynthetic leaves are triangular or semi-circular needle-like, and grow in whorls on secondary or tertiary compact dwarf shoots. By comparison, J. flaccida juvenile leaves are decurrent and needle-like, and adult leaves are compact, short and scale-like. Comparative analyses were performed to evaluate differences in anatomy and gene expression patterns between developmental phases in both species. RNA from twelve samples was sequenced and analyzed with available software. They were assembled de novo from the RNA-Seq reads. Following assembly, 63,741 high quality transcripts were functionally annotated in P. cembroides and 69,448 in J. flaccida. Evaluation of the orthologous groups yielded 4,140 shared gene families among the four references (adult and juvenile from each species). Activities related to cell division and development were more abundant in juveniles than adults in P. cembroides, and more abundant in adults than juveniles in J. flaccida. Overall, there were 509 up-regulated and 81 down-regulated genes in the juvenile condition of P. cembroides and 18 up-regulated and 20 down-regulated in J. flaccida. Gene interaction network analysis showed evidence of co-expression and co-localization of up-regulated genes involved in cell wall and cuticle formation, development, and phenylpropanoid pathway, in juvenile P. cembroides leaves. Whereas in J. flaccida, differential expression and gene interaction patterns were detected in genes involved in photosynthesis and chloroplast biogenesis. Although J. flaccida and P. cembroides both exhibit leaf heteroblastic development, little overlap was detected and unique genes and pathways were highlighted in this study.

Function, structure, and stability are strongly coupled in obligated oligomers, such as triosephosphate isomerase (TIM). However, little is known about how this coupling evolved. To address this question, five ancestral TIMs (ancTIMs) in the opisthokont lineage were inferred. The encoded proteins were purified and characterized, and spectroscopic and hydrodynamic analysis indicated that all are folded dimers. The catalytic efficiency of ancTIMs is very high and all dissociate into inactive and partially unfolded monomers. The placement of catalytic residues in the three-dimensional structure, as well as the enthalpy-driven binding signature of the oldest ancestor (TIM63) resemble extant TIMs. Although TIM63 dimers dissociate more readily than do extant TIMs, calorimetric data show that the free ancestral subunits are folded to a greater extent than their extant counterparts are, suggesting that full catalytic proficiency was established in the dimer before the stability of the isolated monomer eroded. Notably, the low association energy in ancTIMs is compensated for by a high activation barrier, and by a significant shift in the dimer-monomer equilibrium induced by ligand binding. Our results indicate that before the animal and fungi lineages diverged, TIM was an obligated oligomer with substrate binding properties and catalytic efficiency that resemble that of extant TIMs. Therefore, TIM function and association have been strongly coupled at least for the last third of biological evolution on earth. DATABASES: PDB Entry: 6NEE. ENZYMES: Triosephosphate isomerase 5.3.1.1, Glycerol-3-phosphate dehydrogenase 1.1.1.8.

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.

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.

Despite efforts for a complete phylogeny of Cactaceae, generic circumscription and species level relationships remain unsolved. Within Astrophytum one species is assigned to a different genus (Digitostigma) and two are often treated as a single species (A. myriostigma and A. coahuilense). Astrophytum is endemic to the Chihuahuan Desert, but may also be found in adjacent regions. We reconstructed the phylogeny to date the origin of clades and infer the biogeographic patterns of Astrophytum in order to understand the relationships between group members. Three sequences of chloroplast DNA (rbcL gene, trnL-trnF intergenic spacer, and trnK-matK region) were used with Bayesian and Maximum likelihood methods to generate a phylogeny. Divergence times for each node were estimated using an uncorrelated lognormal clock (BEAST) and inferred ancestral distribution using RASP. Astrophytum is monophyletic, with six species grouped in two main clades. Astrophytum caput-medusae (recognized as Digitostigma) is der...

Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a whole-genome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including a newly assembled genome of Cucurbita argyrosperma, and compared the gene contents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth–death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.

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.

PREMISE OF THE STUDY Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers. METHODS We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation. KEY RESULTS Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal. CONCLUSIONS Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

A plethora of developmental and physiological processes in land plants is influenced by auxin, to a large extent via alterations in gene expression by AUXIN RESPONSE FACTORs (ARFs). The canonical auxin transcriptional response system is a land plant innovation, however, charophycean algae possess orthologues of at least some classes of ARF and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) genes, suggesting that elements of the canonical land plant system existed in an ancestral alga. We reconstructed the phylogenetic relationships between streptophyte ARF and AUX/IAA genes and functionally characterized the solitary class C ARF, MpARF3, in Marchantia polymorpha. Phylogenetic analyses indicate that multiple ARF classes, including class C ARFs, existed in an ancestral alga. Loss- and gain-of-function MpARF3 alleles result in pleiotropic effects in the gametophyte, with MpARF3 inhibiting differentiation and developmental transitions in multiple stages of the life cycle. Although loss-of-function Mparf3 and Mpmir160 alleles respond to exogenous auxin treatments, strong miR-resistant MpARF3 alleles are auxin-insensitive, suggesting that class C ARFs act in a context-dependent fashion. We conclude that two modules independently evolved to regulate a pre-existing ARF transcriptional network. Whereas the auxin-TIR1-AUX/IAA pathway evolved to repress class A/B ARF activity, miR160 evolved to repress class C ARFs in a dynamic fashion.

White pine blister rust (WPBR) is an exotic disease threatening five-needle pines in North America. In spite of its relatively recent introduction, some five-needle pines such as sugar pine (Pinus lambertiana) have developed both complete (major) gene resistance and partial (quantitative) resistance to WPBR. While significant effort has been dedicated to clone and locate the position of the major gene of WPBR resistance in sugar pine, the genetic basis of quantitative resistance remains largely unknown in all Strobus pines. In this work, we took a preliminary approach to identify potential genotype × phenotype associations using the results of long-term survival and symptoms of infection in both experimental and applied breeding populations. Our study found significant associations between several genes and WPBR disease symptoms such as normal active cankers and blights, important symptoms in the development of partial resistance. No significant associations were found with percentage of survival, probably due to the complex inheritance of the disease and long time to infection. With this study, we hope to lay the ground for further genome-wide association studies using large phenotypic data sets in sugar pine and other Strobus pines.

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 (

The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.

Premise of research. Plant sexuality evolves in response to genetic and ecological pressures that shape mating systems and floral traits. Comparing such systems and traits within phylogenies can show evolutionary trends in reproduction and floral morphology without the problems posed by the nonindependence of species. We compared sexual systems in seven species of the monophyletic genus Ariocarpus to elucidate major differences in floral morphology and potential relationships between biogeographic rarity and reproductive traits. We hypothesized that floral morphology would be linked to outcrossing rates and that deviations from strict outcrossing and reduced fertility would be present in rare species.Methodology. In one population per species, floral biology was detailed to characterize breeding systems, and mating systems were determined through pollination treatments. Discriminant analysis was used to identify floral traits that separate flowers into species. Phylogenetically independent contrasts were ...

Demographic and environmental forces shape geographical patterns of genetic diversity. Knowledge thereof is not only important for evolutionary ecologists but, in light of future climate change, will be of interest to conservation biologists as well. Sugar pine (Pinus lambertiana Dougl.) is an ecologically important species found in mixed conifer forests across western North America. We applied a candidate-gene-based environmental study to infer spatial patterns in neutral genetic variation and to identify genetic variants associated with local adaptation to drought. Using a panel of 186 candidate gene single nucleotide polymorphisms (SNP), we genotyped 313 individual trees sampled across the entire state of California, USA. We found evidence for a large-scale subdivision into two genetic clusters along the latitudinal axis and increased genetic similarity among sugar pines within a 200–300-km boundary. Associating allelic to environmental variation indicated nine putative SNPs related to local adaptation to drought. These results provide insights into neutral population structure across the natural range of sugar pine and further substantiated a key role of the mitochondrial import inner membrane machinery in enhanced tolerance to drought and constitute important steps into unravelling the eco-evolutionary dynamics in sugar pine.

The evolution of spermatophyte plants involved fundamental changes in cell wall structure and function which resulted from diversification of carbohydrates and proteins. Cell wall proteomic analyses identified a novel family of proteins of yet unknown function, the DUF642 (Domain of Unknown Function 642) proteins. To investigate the evolution of the DUF642 gene family, 154 gene sequences from 24 plant species were analyzed, and phylogenetic inferences were conducted using the Maximum Likelihood and Bayesian Inference methods. Orthologous genes were detected in spermatophyte species and absent in non-seed known plant genomes. Protein sequences shared conserved motifs that defined the signature of the family. Distribution of conserved motifs indicated an ancestral intragenic duplication event. Gene phylogeny documented paleoduplication events originating three or four clades, depending on root position. When based on mid-point rooting, it retrieved four monophyletic clades: A, B, C, and D. A glycosylphosphatidylinositol (GPI)-anchor site and one or two galactose-binding domains-like (GBDLs) could be predicted for some DUF642 proteins. The B, C, and D clades grouped the predicted GPI-anchored proteins. First evidence of in vitro interaction of a DUF642 protein with a cell wall polysaccharide fraction is provided. A competition assay with cellulose prevented this interaction. The degree of diversification and the conservation of the family suggested that DUF642 proteins are key components in seed plant evolution.

Juniperus blancoi is a rare subtropical conifer with a wide yet restricted distribution and three recognized varieties. In this study, its ecological and genetic exchangeability are tested based on morphological descriptions, habitat differences, size measures, growth form, population genetics estimates and phylogeography, using the trnC-trnD plastid DNA region. Populations show differences in their habitat and morphological characteristics. Phylogeographic structure indicates a complex evolutionary history of expansion, fragmentation, and isolation processes. This resulted in high haplotype diversity (h = 0.863) and differentiation values (Dest = 0.866 and Dest > 0.5 in most pairwise comparisons) and a clear geographic structure with well defined groups. As a consequence, although the species has only 8 known populations, it must be divided into at least five distinct conservation units. Thus protecting a rare species could imply the conservation of a complex evolutionary history of non-exchangeable populations.

†Background and Aims Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas. †Methods Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin. †Key Results In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (RST ¼ 0.671 . permuted RST ¼ 0.101; P , 0.0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima. †Conclusions Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8.

The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.

Pinus pseudostrobus and Pinus montezumae are closely related species. They belong to the subsection Ponderosae, with a wide geographical distribution in Mexico and Central America. Morphological, biochemical, and anatomical information suggests that these species can form hybrids in natural populations. In this study, molecular (chloroplast microsatellites) and morphological markers were studied in 13 natural populations of these species to test the existence of introgressive hybridization, infer its dynamics, and describe the phylogeographic structure of the populations. Using analytical methods of population genetics, as well as Bayesian inference and coalescent approach, we show that putative hybrid populations are more similar to P. pseudostrobus than to P. montezumae and that these populations had the highest estimates of morphological and genetic variation. Furthermore, a greater introgression rate was observed from P. montezumae to putative hybrid and P. pseudostrobus populations. We showed that ge...

Uncovering the genes and molecular basis of phenotypic variation and adaptation is a major goal in conservation and evolutionary genetics; it also sets the basis for future operational breeding in commercial species, like forest trees. These taxa are characterized by their large size, growth habit and longevity, which hampers the use of reverse-genetic approaches (i.e. from gene function to phenotype) to pinpoint adaptive molecular variants. In this chapter, we summarize the basis of the forward-genetic approaches (i.e. from phenotype to gene function) currently used in forest trees. For each strategy, we provide a brief overview of the statistical approaches employed to identify candidate genes, and then highlight the main findings of landmark studies that provide evidence for adaptation in forest trees. Adaptive and commercial traits are generally well inherited in trees, although they are mostly affected by the variation of multiple genes, each one accounting for a small part of the phenotypic variance of each character. However, some individual and important genes involved in growth, phenology, drought resistance and cold hardiness have been identified; many of them showing evidence of selection across multiple taxa (sometimes including angiosperms and gymnosperms). Future challenges for detecting the signatures and understanding the molecular basis of adaptation in trees include more adequate and precise phenotype assessment in natural populations, and the inclusion of gene interactions and epigenetic variations in current models. The implications of these findings in conservation and breeding of forest trees are finally discussed.

In the genus Pinus the internal transcribed spacers (ITS1 and ITS2) and the 5.8s region of the nuclear ribosomal DNA are approximately 3000 bp in length. ITS1 is considerably longer than ITS2 and partial sequences of ITS1 indicate that this region is evolving rapidly and exhibits intraspecific variation. The ITS2 and 5.8s regions are relatively conserved. We surveyed restriction fragment length variability of PCR-amplified fragments (PCR-RFLP) of the ITS region in four populations (86 individuals) of Pinus rzedowskii, a pine endemic to western Michoacan, Mexico. Five of the restriction endonucleases assayed revealed variation, with a total of 13 variants, most of which were length mutations of 300–900 bp. A moderate degree of population differentiation was detected. The average diversity (Shannon’s index) of ITS fragment size patterns was 1.19, with 34% of the variation due to differences among populations and 66% due to differences among individuals within populations. The same individuals were assayed for nine polymorphic isozymes, which gave diversity measures similar to those of each restriction endonuclease.

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar 'Dr. Davis' and a brown rot resistant introgression line, 'F8,1-42', derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot.

PREMISE OF STUDY: Bisexuality (male and female function in one structure) has been reported as a key innovation of angiosperms. Although there are several reports of "teratological" bisporangiate (bisexual) cones in gymnosperms, there have been none on the viability of their ovules and pollen. Analyses of the development and arrangement of female and male structures on bisporangiate cones of Pinus johannis enables us to gain insight on the origin of bisexuality in seed plants, for both angiosperms and gymnosperms. METHODS: Viability of bisporangiate cones was assayed by performing manual crosses and using anatomical and histological methods. KEY RESULTS: We determined that bisporangiate cones of P. johannis produce functional pollen and ovules. Male and female organs occupy basal and apical positions, respectively, the same positions found in almost all bisporangiate strobili in gymnosperms and bisexual flowers in angiosperms. CONCLUSIONS: The viability and spatial distribution of female and male organs of bisporangiate cones and their frequent occurrence in gymnosperms suggest a common mechanism in all seed plants for the production of bisporangiate structures. This idea is further supported by the presence of homologous genes for sexual organ identity in gymnosperms and angiosperms as reported by other authors. The lack of bisporangiate structure in gymnosperms may be primarily due to selection to avoid inbreeding rather than to genetic constraint.

The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law. Keywords: Maize, Teosinte, Maize SNP50K BeadChip, Mexican landraces, Proyecto Global de Maíces Nativos