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Constructing phylogenetic relationships among closely related species is a recurrent challenge in evolutionary biology, particularly for long-lived taxa with large effective population sizes and uncomplete reproductive isolation, like conifers. Conifers further have slow evolutionary rates, which raises the question of whether adaptive or non/adaptive processes were predominantly involved when they rapidly diversified after migrating from temperate regions into the tropical mountains. Indeed, fine-scale phylogenetic relationships within several conifer genus remain under debate. Here, we studied the phylogenetic relationships of endemic firs (Abies, Pinaceae) discontinuously distributed in the montane forests from the Southwestern United States to Guatemala, and addressed several hypotheses related to adaptive and non-adaptive radiations. We derived over 80 K SNPs from genotyping by sequencing (GBS) for 45 individuals of nine Mesoamerican species to perform phylogenetic analyses. Both Maximum Likelihood and quartets-inference phylogenies resulted in a well-resolved topology, showing a single fir lineage divided in four subgroups that coincided with the main mountain ranges of Mesoamerica; thus having important taxonomic implications. Such subdivision fitted a North-South isolation by distance framework, in which non-adaptive allopatric processes seemed the rule. Interestingly, several reticulations were observed within subgroups, especially in the central-south region, which may explain past difficulties for generating infrageneric phylogenies. Further evidence for non-adaptive processes was obtained from analyses of 21 candidate-gene regions, which exhibited diminishing values of π a /π s and K a /K s with latitude, thus indicating reduced efficiency of purifying selection towards the Equator. Our study indicates that non-adaptive allopatric processes may be key generators of species diversity and endemism in the tropics., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Background: The New World leaf-nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown., Results: We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled, and annotated the genomes of five Phyllostomid species: one insect feeder (Macrotus waterhousii), one fruit feeder (Artibeus jamaicensis), and three nectar feeders from the Glossophaginae subfamily (Leptonycteris yerbabuenae, Leptonycteris nivalis, and Musonycteris harrisoni), also including the previously sequenced vampire Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar-feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids., Conclusions: Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content., (© The Author(s) 2020. Published by Oxford University Press.)

The genus Agave sensu lato contains ca. 211 described species, many of which are considered keystone species because of their ecological dominance and the quantity of resources they provide with their massive, nectar-rich inflorescences. The large diversity of Agave species has been hypothesized as being related to their reproductive strategy (predominantly monocarpic) and diverse pollinators (e.g., bats, hummingbirds, hawkmoths). In particular, Agave species provide resources that a few genera of nectar feeding bats from the subfamily Glosophaginae are dependent upon. To explore a possible coevolutionary relationship between Agave and the bat species that pollinate them, we calibrated molecular phylogenies of both groups and looked for a correlation in their dates of divergence. One coding and two non-coding regions of the chloroplast genome were sequenced from 49 species of the Agavoideae (Asparagaceae), and the mitochondrial gene Cyt-b and nuclear coding gene RAG2 were either sequenced or obtained from gene bank for 120 Phyllostomid bats. Results from the analyses indicate that Agave sensu lato is a young genus (estimated crown age 2.7-8.5/stem age 4.6-12.3 Ma), with an increasing diversification rate, and the highest speciation rate among Agavoideae's clades. The origin of the Glossophaginae bats (stem age 20.3-23.5 Ma) occurred prior to the stem age of Agave sensu lato, while the origin of the current pollinators of Agave species, members of the genera Glossophaga, Leptonycteris, Anoura, Choeronyscus, Musonycteris and Choeronycteris, was estimated to be around 6.3-16.2 Ma, overlapping with the stem age of Agave sensu lato, supporting the hypothesis of diffuse coevolution., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Premise of the Study: Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome. Here, we investigate evolutionary relationships of yuccas and closely related genera looking at the timing and origin of yucca moth pollination., Methods: In this study, we sequenced the chloroplast genomes of 20 species in the subfamily Agavoideae (Asparagaceae) and three confamilial outgroup taxa to resolve intergeneric phylogenetic relationships of Agavoideae. We estimated divergence times using protein-coding genes from 67 chloroplast genomes sampled across monocots to determine the timing of the yucca moth pollination origin., Key Results: We confidently resolved intergeneric relationships in Agavoideae, demonstrating the origin of the yucca-yucca moth mutualism on two distinct lineages that diverged 27 million years ago. Comparisons of Yucca and Hesperoyucca divergence time to those of yucca moths (Tegeticula and Parategeticula, Prodoxidae) indicate overlapping ages for the origin of pollinating behavior in the moths and pollination by yucca moths in the two plant lineages., Conclusion: Whereas pollinating yucca moths have been shown to have a single origin within the Prodoxidae, there were independent acquisitions of active pollination on lineages leading to Yucca and Hesperoyucca within the Agavoideae., (© 2016 Botanical Society of America.)

Variation in species richness across regions and between different groups of organisms is a major feature of evolution. Several factors have been proposed to explain these differences, including heterogeneity in the rates of species diversification and the age of clades. It has been frequently assumed that rapid rates of diversification are coupled to high rates of ecological and morphological evolution, leading to a prediction that remains poorly explored for most species: the positive association between ecological niche divergence, morphological evolution and species diversification. We combined a time-calibrated phylogeny with distribution, ecological and body size data for scaly tree ferns (Cyatheaceae) to test whether rates of species diversification are predicted by the rates at which clades have evolved distinct ecological niches and body sizes. We found that rates of species diversification are positively correlated with rates of ecological and morphological evolution, with rapidly diversifying clades also showing rapidly evolving ecological niches and body sizes. Our results show that rapid diversification of scaly tree ferns is associated with the evolution of species with comparable morphologies that diversified into similar, yet distinct, environments. This suggests parallel evolutionary pathways opening in different tropical regions whenever ecological and geographical opportunities arise. Accordingly, rates of ecological niche and body size evolution are relevant to explain the current patterns of species richness in this 'ancient' fern lineage across the tropics., (© 2016 The Author(s).)

Premise of the Study: Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico., Methods: We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages., Key Results: We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya., Conclusions: Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico., (© 2016 Botanical Society of America.)

Background and Aims: Convergent evolution is invoked to explain similarity between unrelated organisms in similar environments, but most evaluations of convergence analyse similarity of organismal attributes rather than of the environment. This study focuses on the globular succulent plants of the Americas, the cacti, and their counterparts in Africa in the ice-plant, spurge and milkweed families. Though often held up as paragons of convergent morphological evolution, the environmental similarity of these plants has remained largely unexamined from a quantitative perspective., Methods: Five hotspots (centres of high species diversity of globular succulents) were selected, two in Mexico and three in South Africa. Their environments were compared using niche modelling tools, randomization tests of niche similarity and multivariate analyses to test for environmental similarity., Key Results: Although the sites selected have 'similar' but unrelated life forms, almost all our results highlighted more climate differences than similarities between the hotspots. Interprediction of niches within and between continents, a niche equivalence test, and MANOVA results showed significant differences. In contrast, a niche similarity test showed that the comparisons of Cuatrociénegas-Richtersveld, Huizache-Knersvlakte and Huizache-Richtersveld were similar., Conclusions: Differences in rainfall and temperature regimes and the potential effect of edaphic factors may be involved in the differences between the hotspots. In addition, differences in structure, morphology and physiology of the globular succulents may coincide with some of the climatic dissimilarities; i.e. given convergence as the evolution of similar morphologies under similar conditions, then it may be that differing environments diagnose inconspicuous morphological differences. Moreover, although fine-scale differences between sites were found, a coarser perspective shows that these sites are clearly similar as drylands with relatively moderate drought and mild temperatures, illustrating how all studies of convergence must address the issue of how similar two entities must be before they are considered convergent.

Background: The species Zea mays includes both domesticated maize (ssp. mays) and its closest wild relatives known as the teosintes. While genetic and archaeological studies have provided a well-established history of Z. mays evolution, there is currently minimal description of its current and past distribution. Here, we implemented species distribution modeling using paleoclimatic models of the last interglacial (LI; ∼135,000 BP) and the last glacial maximum (LGM; ∼21,000 BP) to hindcast the distribution of Zea mays subspecies over time and to revisit current knowledge of its phylogeography and evolutionary history., Methodology/principal Findings: Using a large occurrence data set and the distribution modeling MaxEnt algorithm, we obtained robust present and past species distributions of the two widely distributed teosinte subspecies (ssps. parviglumis and mexicana) revealing almost perfect complementarity, stable through time, of their occupied distributions. We also investigated the present distributions of primitive maize landraces, which overlapped but were broader than those of the teosintes. Our data reinforced the idea that little historical gene flow has occurred between teosinte subspecies, but maize has served as a genetic bridge between them. We observed an expansion of teosinte habitat from the LI, consistent with population genetic data. Finally, we identified locations potentially serving as refugia for the teosintes throughout epochs of climate change and sites that should be targeted in future collections., Conclusion/significance: The restricted and highly contrasting ecological niches of the wild teosintes differ substantially from domesticated maize. Variables determining the distributions of these taxa can inform future considerations of local adaptation and the impacts of climate change. Our assessment of the changing distributions of Zea mays taxa over time offers a unique glimpse into the history of maize, highlighting a strategy for the study of domestication that may prove useful for other species.