Erika Aguirre-Planter

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.

Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala

The genus Abies has a complex history in southern México and Guatemala. In this region, four closely related species, Abies flinckii, A. guatemalensis, A. hickelii, and A. religiosa, are distributed in fragmented and isolated montane populations. Range‐wide genetic variation was investigated across species using cytoplasmic DNA markers with contrasted inheritance. Variation at two maternally inherited mitochondrial DNA markers was low. All species shared two of the nine mitotypes detected, while the remaining seven mitochondrial DNA types were restricted to a few isolated stands. Mitochondrial genetic differentiation across taxa was high (GST = 0.933), it was not related to the taxonomic identity (amova; P > 0.05) of the populations, and it was not phylogeographically structured (GST ≈ NST). In contrast, variation at three paternally inherited chloroplast DNA microsatellites was high. Chloroplast genetic differentiation was lower (GST = 0.402; RST = 0.547) than for mitochondrial DNA, but it was significantly related to taxonomy (amova; P < 0.001), and exhibited a significant phylogeographical structure (GST < RST). Different analyses of population structure indicated that A. flinckii was the most divergent taxon, while the remaining three species formed a relatively homogeneous group. However, a small number of the populations of these three taxa, all located at the limits of their respective ranges or in the Transverse Volcanic Belt, diverged from this main cluster. These trends suggest that the Mesoamerican Abies share a recent common ancestor and that their divergence and speciation is mainly driven by genetic drift and isolation during the warm interglacial periods.

Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context.

The genus Abies is distributed discontinuously in the temperate and subtropical montane forests of the northern hemisphere. In Mesoamerica (Mexico and northern Central America), modern firs originated from the divergence of isolated mountain populations of migrating North American taxa. However, the number of ancestral species, migratory waves and diversification speed of these taxa is unknown. Here, variation in repetitive (Pt30204, Pt63718, and Pt71936) and non-repetitive (rbcL, rps18-rpl20 and trnL-trnF) regions of the chloroplast genome was used to reconstruct the phylogenetic relationships of the Mesoamerican Abies in a genus-wide context. These phylogenies and two fossil-calibrated scenarios were further employed to estimate divergence dates and diversification rates within the genus, and to test the hypothesis that, as in many angiosperms, conifers may exhibit accelerated speciation rates in the subtropics. All phylogenies showed five main clusters that mostly agreed with the currently recognized sections of Abies and with the geographic distribution of species. The Mesoamerican taxa formed a single group with species from southwestern North America of sections Oiamel and Grandis. However, populations of the same species were not monophyletic within this group. Divergence of this whole group dated back to the late Paleocene and the early Miocene depending on the calibration used, which translated in very low diversification rates (r(0.0)=0.026-0.054, r(0.9)=0.009-0.019 sp/Ma). Such low rates were a constant along the entire genus, including both the subtropical and temperate taxa. An extended phylogeographic analysis on the Mesoamerican clade indicated that Abies flinckii and A. concolor were the most divergent taxa, while the remaining species (A. durangensis, A. guatemalensis, A. hickelii, A. religiosa and A. vejari) formed a single group. Altogether, these results show that divergence of Mesoamerican firs coincides with a model of environmental stasis and decreased extinction rate, being probably prompted by a series of range expansions and isolation-by-distance.

Evolution of an Ancient Microsatellite Hotspot in the Conifer Mitochondrial Genome and Comparison with Other Plants

In plants, mitochondrial sequence tandem repeats (STRs) have been associated with intragenomic recombination, a process held responsible for evolutionary outcomes such as gene regulation or cytoplasmic male-sterility. However, no link has been established between the recurrent accumulation of STRs and increased mutation rates in specific regions of the plant mtDNA genome. Herein, we surveyed this possibility by comparing, in a phylogenetic context, the variation of a STR-rich mitochondrial intron (nad5-4) with eleven mtDNA genes devoid of STRs within Abies (Pinaceae) and its related genera. This intron has been accumulating repeated stretches, generated by at least three-independent insertions, before the split of the two Pinaceae subfamilies, Abietoideae and Pinoideae. The last of these insertions occurred before the divergence of Abies and produced, exclusively within this genus, a tenfold increase of both the indel and substitution rates in the STR hotspot of the intron. The regions flanking the STRs harbored mutation rates as low as those estimated in mitochondrial genes devoid of repeated stretches. Further searches in complete plant mtDNA genomes, and previous studies reporting polymorphic mtSTRs, revealed that repeated stretches are common in all sorts of plants, but their accumulation in STR hotspots appears to be taxa specific. Our study suggests a new mutagenic role for repeated sequences in the plant mtDNA.

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 (<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.

Genetics and Ecology of Wild and Cultivated Maize: Domestication and Introgression

Maize (Zea mays subspecies mays) has been culturally and economically a very important crop since it was domesticated from its wild relatives, the teosintes (both the lowlands teosinte, Zea mays subspecies parviglumis and the highlands teosisnte, Zea mays subspecies mexicana) in Mexico. In this chapter, we review molecular studies analyzing different aspects of the genetic resources, domestication, phylogeography, and other aspects of the evolution of maize and teosintes, including niche modeling. The genetic studies range from isoenzymes to single nucleotide polymorphisms and other genomic and transcriptomic studies. Both cultivated maize and wild teosintes have high levels of genetic variation and signals of strong local adaptation. Currently, the most accepted hypothesis on maize origin indicates that domestication occurred 9000 years ago in a single event in southern Mexico from the lowland subspecies, Z. m. parviglumis. According to these ideas, later maize spread into higher elevations through adaptive introgression with highland teosintes, Z. m. mexicana. But these ideas are still open to discussion, as better data are needed. Since the origin of maize, there has been strong ongoing artificial selection that has allowed maize to diversify and spread globally and to highly new environments. This intensive selection in maize has left strong molecular signals of selection on a variety of genes that go from domesticated genes to improvement genes. To help respond to climate and global changes, it will be important to determine genes of agronomic importance for tolerance (weather, plagues) and improvement (increase in productivity) to cope with these changes.

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.