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Summary• Here, we performed phylogenetic analyses and estimated the divergence times on mostly sympatric populations of five species within subgenus Nothofagus. We aimed to investigate whether phylogenetic relationships by nuclear internal transcribed spacer (ITS) and phylogeographic patterns by chloroplast DNA (cpDNA) mirror an ancient evolutionary history that was not erased by glacial eras. Extant species are restricted to Patagonia and share a pollen type that was formerly widespread in all southern land masses. Weak reproductive barriers exist among them.• Fifteen cpDNA haplotypes resulted from the analysis of three noncoding regions on 330 individuals with a total alignment of 1794 bp. Nuclear ITS data consisted of 822 bp. We found a deep cpDNA divergence dated 32 Ma at mid-latitudes of Patagonia that predates the phylogenetic divergence of extant taxa. Other more recent breaks by cpDNA occurred towards the north.• Complex paleogeographic features explain the genetic discontinuities. Long-lasting paleobasins and marine ingressions have impeded transoceanic dispersal during range expansion towards lower latitudes under cooler trends since the Oligocene.• Cycles of hybridization-introgression among extant and extinct taxa have resulted in widespread chloroplast capture events. Our data suggest that Nothofagus biogeography will be resolved only if thorough phylogeographic analyses and molecular dating methods are applied using distinct genetic markers.

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Phylogeographic studies have made a significant contribution to the interpretation of genetic lineage distribution in response to climate changes, such as during glaciation events of the Neogene. However, the effects of ancient landscapes associated with global sea level rises, tectonic processes, and climatology driving lineage evolution have been largely overlooked. These effects can be tested in widespread lineages of cold-tolerant species that have endured cooling, and thus, phylogeographic patterns may reflect large-scale processes that were not reset by the ice ages. We hereby combine geological evidence from marine sedimentary basins, Andean orogeny, and climatology with molecular dating and statistical phylogeography to infer how geological and climatic processes affected the distribution of lineages in cold-tolerant Nothofagus species during the Cenozoic. A total of 239 populations along the entire range of all species within the genus Nothofagus (N. antarctica, N. betuloides, N. dombeyi, N. nitida, and N. pumilio) were sampled and analyzed by sequencing three non-coding regions of the chloroplast. We found 30 chloroplast DNA haplotypes that were geographically structured. Molecular dating calibrated with fossils revealed that ancestral lineages appeared in Eocene/Oligocene, whereas most divergences took place during the Miocene; in turn, Bayesian skyline plots showed that population expansion occurred in the Early Pleistocene (1.5-1 million years ago). Lineage divergence from all wide-ranging Nothofagus was spatially and temporally concordant with episodic marine transgressions and warmer times in Patagonia during Eocene/Miocene Epochs. Long-lasting stable raised areas preserved haplotype diversity throughout Patagonia, from where cold-tolerant taxa expanded their ranges during pre-Quaternary times. The detailed study of such ancient divergences is novel and allows us to infer the effects of geological processes on distribution patterns of ancient lineages, that is, phylogeology.

Nierembergia (Solanaceae) contains 21 species found primarily in South America, with one species occurring disjunctly in Mexico. Among other features, a pollination system not found elsewhere in the Solanaceae typifies this genus. In most species, nectaries are absent, but oil-producing elaiophores are present on the corolla limb and these attract oil-collecting bees. Molecular phylogenetic hypotheses based on nuclear ITS and chloroplast rpl16 intron data support the monophyly of Nierembergia, which is sister to a clade composed of Bouchetia plus Hunzikeria. The data reconstruct two clades within the genus: one composed primarily of herbaceous species with broad stigmas and the second containing woody species with crescent-shaped stigmas. Morphological homoplasy is frequent among the species of the herbaceous clade, while the woody clade is morphologically cohesive. Chromosome counts are confirmed and karyotype features are given for 13 Nierembergia species (including six varieties) and for Bouchetia anomala, Leptoglossis linifolia, and Petunia axillaris. The two clades are also supported by karyotypic features: one has asymmetrical karyotypes, small chromosomes, and two chromosome pairs with nucleolar organizing regions (NOR) and the other has symmetrical karyotypes, large chromosomes, and only one NOR.

Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species.

Fluorescent chromosome banding and measurements of nuclear DNA content by image cytometry of Feulgen-stained cells were performed in one sample each of eight diploid (2n = 24) species of Solanum:

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