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Aim: Previous population genetic and phylogeographical studies have shown how generation time and dispersal affect population divergence in the presence of a vicariant barrier. More recently, speciation genomic studies have revealed that selection and recombination can be equally impactful. Here, we test how the interaction of these factors shapes the divergence expected in response to an ephemeral barrier and compare these results to empirical literature using the Baja California peninsula as a test case. Location: Global. Taxon: Diploid eukaryotes. Methods: We forward simulated population genomic data with CDMetaPOP and SLiM by varying dispersal rate, mutation rate, generation time, selection pressure and recombination in the presence and then removal of a physical barrier. We tested which factors affect the divergence signal (measured as FST). We compared simulation results to empirical literature that included 147 records of generation times and 78 divergence estimates from population genomic studies. Results: Population differentiation not only occurred due to the presence of a barrier under lower dispersal abilities but also emerged as a result of low dispersal among structured populations without a barrier. Divergent selection strengthened differentiation, which is supported by empirical data. Barrier removal quickly eroded the divergence signal (~500 generations) for high‐dispersing species, but low dispersal species retained divergence after gene flow resumed. In the empirical data, generation times varied by four orders of magnitude and dispersal by three orders of magnitude. Main Conclusions: Divergence can arise without vicariant barriers, it may not produce a tight co‐divergence peak in absolute time, and co‐divergence may not imply a common cause of divergence. Deeper integration of geologic, climatic and genomic data (i.e. geogenomics) may help clarify origins of divergence in physically complex settings. [ABSTRACT FROM AUTHOR]

Aim: In geographically and ecologically heterogeneous landscapes, such as tropical mountains, widely distributed species may be informative proxies for studying landscape and climatic evolution. We explore historical vicariant and dispersal processes that may have determined the genetic structure and variation of a palm species complex living in cloud forests. We hypothesize that the genomic groupings reflect uplift‐based isolation by vicariance, divergence via dispersal events driven by faulted montane segments or recent divergence due to climate fluctuations. Location: Colombian Andes. Taxon Geonoma undata–G. orbignyana species complex (Arecaceae). Methods: We sampled 195 individuals of the species complex plus the outgroup (G. interrupta) across the three cordilleras of Colombia, the Colombian Massif and the Sierra Nevada de Santa Marta. We used target capture sequencing to generate a dataset of 12,750 quality‐filtered genome‐wide SNPs. We conducted phylogenetic, multivariate and population genomics and structure analyses to infer demographical history. Results: We found four genetically distinct groups within the species complex. The geographical distributions of the genetic groups, and their inferred phylogenetic and population divergence are consistent with a history of colonization of mountain segments that were disconnected until the late Pliocene. These breaks coincide with the distribution of Pliocene strike‐slip faulting events. Main conclusions The faulting and resultant topographic disruption of the northernmost Andean cordillera prior to the onset of the Pleistocene is implied by the presence of phylogeographic breaks in areas that are topographically continuous today. These cordilleras were formed by connecting segments that were previously uplifted but historically detached in areas where dense fault systems occur. Large‐scale strike‐slip faulting can generate topographic gaps, features that likely caused the divergence by dispersal with gene flow of the Geonoma undata–G. orbignyana complex. [ABSTRACT FROM AUTHOR]

The topographic gradients of the Tropical Andes may have triggered species divergence by different mechanisms. Topography separates species' geographical ranges and offers climatic heterogeneity, which could potentially foster local adaptation to specific climatic conditions and result in narrowly distributed endemic species. Such a pattern is found in the Andean centered palm genus Aiphanes. To test the extent to which geographic barriers and climatic heterogeneity can explain distribution patterns in Aiphanes , we sampled 34 out of 36 currently recognized species in that genus and sequenced them by Sanger sequencing and/or sequence target capture sequencing. We generated Bayesian, likelihood, and species-tree phylogenies, with which we explored climatic trait evolution from current climatic occupation. We also estimated species distribution models to test the relative roles of geographical and climatic divergence in their evolution. We found that Aiphanes originated in the Miocene in Andean environments and possibly in mid-elevation habitats. Diversification is related to the occupation of the adjacent high and low elevation habitats tracking high annual precipitation and low precipitation seasonality (moist habitats). Different species in different clades repeatedly occupy all the different temperatures offered by the elevation gradient from 0 to 3,000 m in different geographically isolated areas. A pattern of conserved adaptation to moist environments is consistent among the clades. Our results stress the evolutionary roles of niche truncation of wide thermal tolerance by physical range fragmentation, coupled with water-related niche conservatism, to colonize the topographic gradient. [ABSTRACT FROM AUTHOR]

Genetic diversity is key in providing the variation needed to face stochastic change. Increased habitat loss alters population size and dynamics posing serious threats to the conservation of wild species. Colombia has undergone massive deforestation over the last century, but harbors extraordinary high species diversity of genus Zamia (Cycadales); however, most of the species are under threat. In this study, we targeted the largest accessible remaining populations of 2 closely related species growing as endemics in the Magdalena Valley region of Colombia. We successfully transferred the SSR loci used in previous Zamia studies to these species. In total, we amplified 13 microsatellite loci in 3 wild populations, aiming at: 1) assessing genetic diversity and 2) understanding if the structure found between the 3 populations reflected species and population boundaries due to ecological and historical genetic isolation. We found that the actual population size does not reflect population genetic diversity with a small population (Perales) harboring the highest genetic diversity. In addition, all populations are highly structured regardless of species containment, all showing signs of genetic isolation. Given the high degree of ecological threat, and the inherent biological traits of Cycads, we provide information regarding the prioritization of populations for ex situ management. [ABSTRACT FROM AUTHOR]

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Given the geographical complexity of the Andes, species distributions hold interesting information regarding the history of isolation and gene flow across geographic barriers and ecological gradients. Moreover, current threats to the region's enormous plant diversity pose an additional challenge to the understanding of these patterns. We explored the geographic structure of genetic diversity within the Ceroxylon quindiuense species complex (wax palms) at a regional scale, using a model-based approach to disentangle the historical mechanisms by which these species have dispersed over a range encompassing 17° of latitude in the tropical Andes. A total of 10 microsatellite loci were cross-amplified in 8 populations of the 3 species comprising the C. quindiuense complex. Analyses performed include estimates of molecular diversity and genetic structure, testing for genetic bottlenecks and an evaluation of the colonization scenario under approximate Bayesian computation. We showed that there was a geographical diversity gradient reflecting the orogenetic pattern of the northern Andes and its end at the cordilleras facing the Caribbean Sea. A general pattern of diversity suggests that the cordilleras of Colombia have served as historical recipients of gene flow occurring only scantly along the northern Andes. We provided evidence of important isolation between the largest populations of this complex, suggesting that both historical constraints to dispersal but also current anthropogenic effects might explain the high levels of population structuring. We provide a list of advisable measures for conservation stakeholders. [ABSTRACT FROM AUTHOR]

A review of the tallest non-climbing palms around the world reveals 52 species that reach up to 30 m, and only 19 species that reach 35 m or higher. Both the largest documented measurements and the largest number of records confirm the Quindío wax palm of Colombia, Ceroxylon quindiuense, as the world’s tallest species in the family. The Caribbean Roystonea oleracea ranks second tallest, and the Malesian Pigafetta elata and Pigafetta filaris tie for third place. [ABSTRACT FROM AUTHOR]

Wax palms are an important element of the cloud forests in the tropical Andes. Despite heavy deforestation, the density of adults seems to be similar in deforested pastures as in forests. We aimed to infer the mechanisms responsible for this apparent resilience in pastures and we tested two hypotheses to explain it: 1) adult palms survived in pastures because they were spared from logging, and 2) adults occurred in pastures through the resilience of large juvenile rosettes, which survived through subterranean meristems and later developed into adults. For this purpose, we characterized the demographic structure of C. quindiuense in a total of 122 plots of 400 m2 in forests and pastures at two sites with contrasted land use histories in Colombia and Peru. Additionally, we implemented growth models that allowed us to estimate the age of individuals at four sites. These data were combined with information collected from local land managers in order to complete our knowledge on the land use history at each site. At two sites, the presence of old individuals up to 169 years and a wide age range evidenced that, at least, a portion of current adults in pastures were spared from logging at the time of deforestation. However, at the two other sites, the absence of older adults in pastures and the narrow age range of the populations indicated that individuals came exclusively from rosette resilience. These interpretations were consistent with the land use history of sites. In consequence, the combination of the two hypotheses (spared individuals and rosette resilience) explained patterns of C. quindiuense in pastures on a regional scale. Regeneration through subterranean meristems in palms is an important, yet overlooked mechanism of resilience, which occurs in a number of palm species and deserves being integrated in the conceptual framework of disturbance ecology. [ABSTRACT FROM AUTHOR]