Choice of molecular marker influences spatial patterns of phylogenetic diversity.

Spatial patterns of phylogenetic diversity (PD) are increasingly becoming relevant for conservation decisions. PD measures are based on phylogenies estimated from molecular data. This paper addresses the question of how different molecular markers impact PD spatial patterns. We first conducted a simple simulation to explore the effect of deep and shallow changes in topology (simulating variations in molecular markers), using ultrametric and non-ultrametric trees, and then used a dataset of Chilean flora with four sets of markers to assess potential differences in spatial patterns of PD ranks using different markers and types of trees. The simulation consistently showed that the difference in PD rank was lower for ultrametric trees than for phylograms. A similar trend was observed using the Chilean flora dataset, with among-markers variability in spatial patterns of the PD metrics lower for ultrametric than for non-ultrametric trees, depicted as top 2.5 and 5% hotspots. Frequency distribution of PD values differed among markers as well, with this variation less apparent for ultrametric trees. We conclude that the choice of markers impacts spatial patterns of PD, and these results vary more strongly for phylograms, suggesting that ultrametric trees are more robust to the choice of marker.

Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores.

BACKGROUND AND AIM: Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales. METHODS: We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70% of Bocageeae species, covering its geographic range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework. KEY RESULTS: The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Its ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico, during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes. CONCLUSIONS: In Bocageeae mammals may have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal may have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity, and abundance at particular time periods and places. Hence, inter- and intracontinental dispersal may not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.

Plant migration under long-lasting hyperaridity - phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth.

The post-Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae). We analyze phylogenetic relationships and historical biogeography by using next-generation sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas. Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene. We show that NGS combined with near-comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases.

Fruit evolution in Hydrophyllaceae.

PREMISE: Fruit type and morphology are tightly connected with angiosperm diversification. In Boraginales, the first-branching families, including Hydrophyllaceae, have one- to many-seeded capsules, whereas most of the remaining families have four-seeded indehiscent fruits. This fact argues for many-seeded capsules as the ancestral condition. However, little is known about the evolution of fruit dehiscence and seed number. The present study investigated the gynoecium and fruit development and morphology and the evolution of seed-numbers in Hydrophyllaceae. METHODS: Gynoecium and fruit development and morphology were studied using scanning electron microscopy and x-ray microcomputed tomography. Ancestral character state reconstruction of seed number was performed using a broadly sampled phylogeny of Boraginales (ndhF and ITS) with an emphasis on Hydrophyllaceae. RESULTS: Our ontogenetic studies not only demonstrate parallel developmental trajectories across Hydrophyllaceae, but also a striking diversity regarding the internal organization of the gynoecium. Ovule number appears to determine ovary structure. Many-seeded capsules are retrieved as the ancestral state of Hydrophyllaceae. At least seven transitions to fruits with (one to) four seeds and four reversals (i.e., from four- to many-seeded fruits) were reconstructed in Hydrophyllaceae. CONCLUSIONS: Several shifts in seed number from "many" to "four" and back to "many" have taken place in capsular-fruited Hydrophyllaceae, a strikingly high number considering that seed number is virtually conserved across the rest of the order. The groups with a conserved seed number of four are characterized by indehiscent schizocarps or drupes and by seeds that are integrated into mericarps. This functional integration probably acts as an evolutionary constraint to shifts in seed number.

Evidence for Middle Miocene origin and morphological evolutionary stasis in a Barbacenia Inselberg clade (Velloziaceae).

Atlantic Forest Inselbergs (AFI) and Campos Rupestres (CR) are mountains and highlands of eastern South America, relatively poorly studied and highly threatened, which display extraordinary levels of plant endemism and richness. In spite of their geographical and environmental differences, the origin of the flora of CR and AFI are likely linked to each other, because several plant clades are distributed across both ecosystems. In addition to these studies, little has been investigated about the historical biogeographical connections between AFI and CR and most evolutionary studies are restricted to CR. Barbacenia (Velloziaceae) is widely spread and nearly endemic to the AFI and CR outcrops and thus represent an ideal system to study the biogeographical connections between CR and AFI. Besides, given the remarkable diversity of Barbacenia in CR compared to AFI, it appears that different factors were important drivers in the diversification of Barbacenia lineages, likely leading to different patterns of morphological diversification. Here, we integrate phylogenetic, biogeographic and morphological approaches to: (i) address whether AFI species of Barbacenia are monophyletic and thus a single colonization of AFI can be inferred; (ii) understand the timing and geographical origin of CR and AFI clades; (iii) compare morphological diversity between Barbacenia from AFI and CR under the hypothesis that these two systems have experienced similar levels of morphological diversification during their evolutionary history. To this end, we presented a phylogeny inferred using plastid (atpB-rbcL, trnH-psbA and trnL-trnF) and nuclear (ITS) markers and a complete sampling of AFI Barbacenia, estimated divergence times, reconstructed the ancestral areas of Barbacenia clades and compared their morphological diversity based on a dataset of 16 characters. Our results provided evidence for a diversification of Barbacenia from the Middle Miocene to Pleistocene, as suggested in previous studies. We suggest that stepping-stone dispersal across mountaintops in interplay with paleovegetation dynamics during the global Miocene cooling and Pleistocene climatic oscillations may played an important role in the range expansion of modern AFI Barbacenia lineages. Finally, our results also showed a significant differences in morphological diversity between AFI and CR clades, suggesting a long-term morphological stasis in AFI species.

Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation.

Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.

Quaternary diversification of a columnar cactus in the driest place on earth.

PREMISE: The cactus family (Cactaceae) is a speciose lineage with an almost entirely New World distribution. The genus Eulychnia with eight currently recognized species is endemic to the Atacama and Peruvian Deserts. Here we investigated the phylogeny of this group based on a complete taxon sampling to elucidate species delimitation and biogeographic history of the genus. METHODS: A family-wide Bayesian molecular clock dating based on plastid sequence data was conducted to estimate the age of Eulychnia and its divergence from its sister genus Austrocactus. A second data set obtained from genotyping by sequencing (GBS) was analyzed, using the family-wide age estimate as a secondary calibration to date the GBS phylogeny using a penalized likelihood approach. Ancestral ranges were inferred employing the dispersal extinction cladogenesis approach. RESULTS: Our GBS phylogeny of Eulychnia was fully resolved with high support values nearly throughout the phylogeny. The split from Austrocactus occurred in the late Miocene, and Eulychnia diversified during the early Quaternary. Three lineages were retrieved: Eulychnia ritteri from Peru is sister to all Chilean species, which in turn fall into two sister clades of three and four species, respectively. Diversification in the Chilean clades started in the early Pleistocene. Eulychnia likely originated at the coastal range of its distribution and colonized inland locations several times. CONCLUSIONS: Diversification of Eulychnia during the Pleistocene coincides with long periods of hyperaridity alternated with pluvial phases. Hyperaridity caused habitat fragmentation, ultimately leading to speciation and resulting in the current allopatric distribution of taxa.

Notes on the genus Ophryosporus (Asteraceae, Eupatorieae) in Chile.

Ophryosporus Meyen is reviewed for Chile and an updated species list for the country based on herbarium records and literature review is presented. A key to the Chilean species is provided and a distribution range of taxa is indicated based on herbarium records and our own collections. We include several lectotypifications as well as an epitypification of Ophryosporus hoppii. The presence of two species, O. hoppii and O. floribundus, formerly accepted for Chile, is questioned and their actual distribution discussed.

ResumenSe revisa el género Ophryosporus para Chile y se presenta una lista actualizada de especies para el país basada en registros de herbario y una revisión de la literatura. Se proporciona una clave para las especies chilenas y se indica el rango de distribución de los taxones basado en registros de herbario. Se cuestiona la presencia de dos especies, O. hoppii y O. floribundus, anteriormente aceptadas para Chile, y se discute su distribución real.

Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications.

Asterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes and combined them with other data sets, representing all accepted orders and nearly all families of asterids. We show fully supported monophyly of asterids, Berberidopsidales as sister to asterids, monophyly of all orders except Icacinales, Aquifoliales, and Bruniales, and monophyly of all families except Icacinaceae and Ehretiaceae. Novel taxon placements benefited from the expanded sampling with living collections from botanical gardens, resolving hitherto uncertain relationships. The remaining ambiguous placements here are likely due to limited sampling and could be addressed in the future with relevant additional taxa. Using our well-resolved phylogeny as reference, divergence time estimates support an Aptian (Early Cretaceous) origin of asterids and the origin of all orders before the Cretaceous-Paleogene boundary. Ancestral state reconstruction at the family level suggests that the asterid ancestor was a woody terrestrial plant with simple leaves, bisexual, and actinomorphic flowers with free petals and free anthers, a superior ovary with a style, and drupaceous fruits. Whole-genome duplication (WGD) analyses provide strong evidence for 33 WGDs in asterids and one in Berberidopsidales, including four suprafamilial and seven familial/subfamilial WGDs. Our results advance the understanding of asterid phylogeny and provide numerous novel evolutionary insights into their diversification and morphological evolution.

Different Predictors Shape the Diversity Patterns of Epiphytic and Non-epiphytic Liverworts in Montane Forests of Uganda.

We studied the influence of regional and local variables on the liverwort diversity within natural forest vegetation of Uganda to contribute to our understanding of the mechanisms and processes determining species richness. To this end, we compared the species richness distribution patterns of epiphytic and non-epiphytic liverworts (Marchantiophytina) in 24 plots in the forests of four Ugandan national parks. We recorded a total of 119 species and subspecies from 18 families, including 16 new species records for the country. We used generalized linear models (GLMs) and the relative variable importance of regional and local climatic and environmental variables to assess their respective impact on the species diversity. We found that the richness patterns of total and epiphytic richness were largely driven by regional climatic factors related to temperature and water-availability. In contrast, species diversity of non-epiphytic and rare species was additionally strongly determined by local-scale microhabitat factors such as height of forest canopy and slope inclination, reflecting the availability of suitable microhabitats. We conclude that macroclimatic variables perform well in predicting epiphytic liverwort richness, whereas the adequate prediction of non-epiphytic richness requires site-specific variables. Also, we propose that richness of epiphytic liverworts will be impacted more directly by climate change than richness of non-epiphytic and rare species.

Plant life at the dry limit-Spatial patterns of floristic diversity and composition around the hyperarid core of the Atacama Desert.

Extreme arid conditions in the Atacama Desert in northern Chile have created a unique vegetation almost entirely restricted to the desert margins along the coast of the Pacific Ocean and the Andean range. In this study we provide data on the desert vegetation along elevational gradients at four localities from the western Andean slopes, between 19° and 21° S. Additionally, zonation of floristic data was explored. Three altitudinal zones could be classified and described in detail for each locality. Conspicuously divergent floras in the Atacama Desert have been recorded in the coastal 'lomas formations' and in the Andean desert vegetation, separated by a narrow band of absolute desert. In this study, we investigate the floristic relationships between both regions by implementing similarity analyses for 21 localities from the coastal and Andean deserts in northern Chile. Our results show a drastic east-west divergence in pairwise floristic similarity, which is in stark contrast to a weaker north-south divergence. A biotic barrier, preventing plant exchange from east to west and vice versa, imposed by the hyperarid conditions of the absolute desert, is one possible explanation for this finding. Moreover, the coastal and Andean deserts likely represent ecologically divergent habitats, e.g., in rainfall seasonality. Essential differences in factors determining plant life between both regions have probably contributed to a divergent evolution of the floras. Both explanations-ecological divergence and ecogeographical isolation-are not mutually exclusive, but likely complementary. We also combined floristic data from northern Chile and southern Peru. Similarity analyses of this combined dataset provide first floristic evidence for the existence of a biotic north-south corridor along the western slope of the Andes. Sub-Andean distributions of several species are discussed in the light of floristic connectivity between the Peruvian and Chilean Andean floristic clusters.

Phylogeny and historical biogeography of Lithospermeae (Boraginaceae): Disentangling the possible causes of Miocene diversifications.

Studies about the drivers of angiosperm clade diversifications have revealed how the environment continuously alters the species chances to adapt or to go extinct. This process depends on complex interactions between abiotic and biotic factors, conditioned to the geological and tectonic settings, the genetic variability of species and the rate at which speciation occurs. In this study, we aim to elucidate the timing of diversification of the Lithospermeae, the second largest tribe within Boraginaceae, and to identify the possible morphological and ecological characters associated with shifts in diversification rates of the most species-rich clades. Lithospermeae includes ca. 470 species and 26 genera, among which are some of the largest genera of the family such as Onosma (150 spp.), Echium (60 spp.), and Lithospermum (80 spp.). An exhaustive study of the whole clade is not available to date and its evolutionary history and diversification rates are incompletely known. In the present study, we provide the most comprehensive phylogeny of the group so far, sampling 242 species and all 26 genera. We found that crown-groups and diversification rates of Lithospermeae largely date back to the Mid-Miocene, with high diversification rates in the largest genera, though only significantly high in Onosma. Our analysis fails to associate any of the functional or morphological traits considered with significant shifts in diversification rates. The timing of the diversification of the species-rich clades corresponds with Miocene tectonic events and global climate changes increasing aridity across Eurasia and western North America. These results suggest a causal link between known ecological features of Lithospermeae (i.e., pre-adaptation to arid, open habitats, and mineral soils) and their diversification. Future studies should expand the sampling of individual subclades and detailed functional analyses to identify the contribution of adaptations to arid conditions and pollinator shifts.

Major lineages of Loasaceae subfam. Loasoideae diversified during the Andean uplift.

The Loasoideae is the largest clade in the Loasaceae. This subfamily is widespread throughout the Neotropics and centered in the Andes, presenting an excellent opportunity to study diversification across much of temperate and mid to high-elevation areas of South America. Despite that, no studies have addressed the historical biogeography of the Loasoideae to date, leaving an important knowledge gap in this plant group. Here, we used four plastid markers (i.e., trnL-trnF, matK, trnS-trnG, and rps16) and sequenced 170 accessions (134 ingroup taxa) to infer the phylogeny of Loasoideae. We then used this phylogeny as basis to estimate divergence times using an uncorrelated relaxed molecular clock approach and seven fossils as primary calibration points. We employed the Dispersal-Extinction-Cladogenesis (DEC) approach to reconstruct the ancestral ranges of the subfamily. Our results indicate that stem Loasoideae diverged from its sister group in the Late Cretaceous to Early Paleocene (ca. 83-62 Ma). The crown node of the whole clade goes back to the Middle Paleocene to Middle Eocene (ca. 60-45 Ma), corresponding to the earliest diversification events of the extant groups, prior to most of the Andean orogeny and roughly coinciding with the Paleocene-Eocene Thermal Maximum. On the other hand, the crown nodes of most genera appear to have originated in the Oligocene and Miocene (median ages: 28-10 Ma). The diversification of some extant lineages appears to have happened in parallel to Andean uplift pulses that seem to have had an effect on the orogeny and concomitant establishment of new habitats and latitudinal corridors. The most likely ancestral areas retrieved for crown Loasoideae, are the tropical Andes and Pacific arid coast. Most of the extant clades have remained restricted to their ancestral areas. Transoceanic Long Distance Dispersal appears to have been involved in the arrival of Loasoid ancestors to South America, and in the distribution of the small clades Kissenia in Africa and Plakothira on the Marquesas Archipelago. The results presented here suggest that the historical biogeography of the continental scale radiation of Loasoideae, follows the sequence and timing of the development of temperate and mid to high-elevation habitats across South America during the Tertiary.

The taxlist package: managing plant taxonomic lists in R.

Taxonomic lists are crucial elements of vegetation-plot databases and provide the links between original entries, reference taxon views and different taxon concepts. We introduce the R package taxlist in the context of object-oriented modelling for taxonomic lists. This package provides a data structure based on species lists in Turboveg, which is a software broadly used for the storage of vegetation-plot databases and implements functions for importing and handling them prior to statistical analysis. We also present a schema for relational databases, compatible with taxlist objects and recommend its use for handling diversity records.

Genomic Resources Notes accepted 1 April 2015 - 31 May 2015.

This article documents the public availability of transcriptomic resources for (i) the stellate sturgeon Acipenser stellatus, (ii) the flowering plant Campanula gentilis and (iii) two endemic Iberian fish, Squalius carolitertii and Squalius torgalensis.

Synopsis of Plazia Ruiz & Pav. (Onoserideae, Asteraceae), including a new species from northern Peru.

A synopsis of Plazia Ruiz & Pav. (Onoserideae, Asteraceae) is presented, including the description of a new species, Plazia robinsonii M.O.Dillon & Sagást., from a locality c. 20 kms west of Huamachuco, Department of La Libertad in northern Peru. It most closely resembles Plazia conferta Ruiz & Pav., a narrow endemic from central Peru some 450 km to the south; however, the latter species has larger leaves and smaller capitula. Plazia is a small genus of four species confined to the Andean Cordillera of Peru, Bolivia, Chile, and Argentina. A distribution map of the four species, an illustration of the new species, a photograph of the holotype, and a key to species are provided.

ResumenSe presenta una sinopsis del género Plazia Ruiz & Pav. (Onoserideae, Asteraceae), incluyendo la descripción de una nueva specie, Plazia robinsonii M.O.Dillon & Sagást., proveniente de una localidad c. 20 km al oeste de Huamachuco, Departamento de La Libertad, norte de Perú. Esta especie es similar a Plazia conferta Ruiz & Pav., un endemismo del centro de Perú, unos 450 km hacia el sur; sin emabrgo, esta última especie tiene hojas más grandes y capítulos más pequeños. Plazia es un género compuesto por cuatro especies restringidas a la Cordillera de los Andes de Perú, Bolivia, Chile y Argentina. Se inlcuye un mapa de distribución de las cuatro especies, una ilustración de la nueva especie, una fotografía del holotipo y una clave para las especies.