The Never-ending Story: Multigene Approaches to the Phylogeny of Amaryllidaceae

a whole, strongly supported the mostly African tribe Amaryllideae as sister to the rest of the family, and resolved geographically-based monophyletic groups, but failed to resolve the relationships among several basal lineages in the family (the African Haemantheae and Cyrtantheae, the Australasian Calostemmateae, and the American and Eurasian sister clades). We present analysis of plastid ndhF sequences that fully resolved the major clades of the family. The baccate-fruited Haemantheae and Calostemmateae are sister tribes, and the African endemic Cyrtantheae is sister to them both. This clade is sister to an American/Eurasian clade. We also present preliminary nuclear ribosomal ITS sequence analysis of the Eurasian clade. Lycorideae are basal in the group and begin a grade that continues with Hannonia, then Pancratium, then Lapiedra. The genera Galanthus, Narcissus, and Sternhergia are resolved as monophyletic with strong support. Leucojum is paraphyletic and recognition of Acis for the mostly autumn-flowering Mediterranean species is supported. Recent phylogenetic analyses of various tribes and genera of the family are reviewed. Above the family level, Agapanthaceae, Alliaceae, and Amaryllidaceae form a well-supported monophyletic group, but exact resolution of the relationships among the three subclades varies depending on the sequence matrix utilized. The Angiosperm Phylogeny Group II has advocated combining all three into a single family, Alliaceae. We discuss this decision, which has historical precedent, but recommend that Amaryllidaceae be conserved as the name for the family in such a treatment

The age of chocolate: A diversification history of Theobroma and Malvaceae

Dated molecular phylogenies of broadly distributed lineages can help to compare patterns of diversification in different parts of the world. An explanation for greater Neotropical diversity compared to other parts of the tropics is that it was an accident of the Andean orogeny. Using dated phylogenies, of chloroplast ndhF and nuclear DNA WRKY sequence datasets, generated using BEAST we demonstrate that the diversification of the genera Theobroma and Herrania occurred from 12.7 (11.6-14.9 [95% HPD]) million years ago (Ma) and thus coincided with Andean uplift from the mid-Miocene and that this lineage had a faster diversification rate than other major clades in Malvaceae. We also demonstrate that Theobroma cacao, the source of chocolate, diverged from its most recent common ancestor 9.9 (7.7-12.9 [95% HPD]) Ma, in the mid-to late-Miocene, suggesting that this economically important species has had ample time to generate significant within-species genetic diversity that is useful information for a developing chocolate industry. In addition, we address questions related to the latitudinal gradient in species diversity within Malvaceae. A faster diversification rate is an explanation for the greater species diversity at lower latitudes. Alternatively, tropical conditions may have existed for longer and occupied greater areas than temperate ones meaning that tropical lineages have had more time and space in which to diversify. Our dated molecular phylogeny of Malvaceae demonstrated that at least one temperate lineage within the family diverged from tropical ancestors then diversified at a rate comparable with many tropical lineages in the family. These results are consistent with the hypothesis that Malvaceae are more species rich in the tropics because tropical lineages within the family have existed for longer and occupied more space than temperate ones, and not because of differences in diversification rate. © 2015 Richardson, Whitlock, Meerow and Madriñán

A remarkable new species of Pamianthe (Amaryllidaceae) from the Department of Cauca, Colombia

A new saxicolous species of Amaryllidaceae tentatively assigned to the tribe Clinantheae, Pamianthe ecollis Silverst., Meerow & Sánchez-Taborda, is described from the western slope of the Cordillera Occidental in the department of Cauca, Colombia. The new species differs from the two hitherto known species of Pamianthe in its yellow flowers and in its nearly obsolete perianth tube. The near loss of the perianth tube may be correlated with a change in pollinator. The new species lacks a bulb; it produces a large number of winged seeds that are wind-dispersed. A key to the species of Pamianthe is provided. This is the first record of the genus Pamianthe for Colombia. The phylogenetic position of the genus Pamianthe is discussed

Beyond bouncing back? Comparing and contesting urban resilience frames in US and Latin American contexts

Urban resilience has gained considerable popularity in planning and policy to address cities’ capacity to cope with climate change. While many studies discuss the different ways that academics define resilience, little attention has been given to how resilience is conceptualized across different urban contexts and among the actors that engage in building resilience ‘on the ground’. Given the implications that resilience frames can have for the solutions that are pursued (and who benefits from them), it is important to examine how transformative definitions of urban resilience are in practice. In this paper, we use data from a survey of nine US and Latin American and Caribbean cities to explore how the concept is framed across multiple governance sectors, including governmental, non-governmental, business, research, and hybrid organizations. We examine these framings in light of recent conceptual developments and tensions found in the literature. The results highlight that, in general across the nine cities, framings converge with definitions of resilience as the ability to resist, cope with, or bounce back to previous conditions, whereas sustainability, equity, and social-ecological-technological systems (SETS) perspectives are rarely associated with resilience. There are noticeable differences across cities and governance actors that point to geographic and political variation in the way resilience is conceptualized. We unpack these differences and discuss their implications for resilience research and practice moving forward. We argue that if resilience is going to remain a major goal for city policies into the future, it needs to be conceived in a more transformative, anticipatory, and equitable way, and acknowledge interconnected SETS

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales—Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P \u3c 10-9) and are each even more strongly associated with shaded habitats (P \u3c 10-10 to 10-23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia

Bioclimatic Architecture and Urban Morphology. Studies on Intermediate Urban Open Spaces

This paper deals with the interactions between biophysical and microclimatic factors on the one hand with, on the other, the urban morphology of intermediate urban open spaces, the relationship between environmental and bioclimatic thermal comfort, and the implementation of innovative materials and the use of greenery, aimed at the users’ well-being. In particular, the thermal comfort of the open spaces of the consolidated fabrics of the city of Rome is studied, by carrying out simulations of cooling strategies relating to two scenarios applied to Piazza Bainsizza. The first scenario involves the use of cool materials for roofs, cladding surfaces, and pavement, while the second scenario, in addition to the cool materials employed in the first scenario, also includes the use of greenery and permeable green surfaces. The research was performed using summer and winter microclimatic simulations of the CFD (ENVI-met v. 3.1) type, in order to determine the dierent influences of the materials with cold colors, trees, and vegetated surfaces on the thermal comfort of the urban morphology itself. Meanwhile, the comfort assessment was determined through the physiological equivalent temperature (PET) calculated with the RayMan program. The first scenario, with the use of cool materials, improves summer conditions and reduces the urban heat island eect but does not eliminate thermal discomfort due to the lack of shaded surfaces and vegetation. The second scenario, where material renovations is matched with vegetation improvements, has a slightly bad eect on winter conditions but drastically ameliorates the summer situation, both for direct users and, thanks to the strong reduction of the urban heat island eect, to urban inhabitants as a whole

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut

BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the "abominable mysteries" of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut. METHODOLOGY/PRINCIPAL FINDINGS:We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree. CONCLUSIONS/SIGNIFICANCE:This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family

Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics

As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and “niu vai” fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent