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Understanding the mechanisms by which the abiotic and biotic requirements of species, or ecological niches, change over time is a central issue in evolutionary biology. Niche evolution is poorly understood at both the macroecological and macroevolutionary scales, as niches can shift over short periods of time but appear to change more slowly over longer timescales. Although reconstructing past niches has always been a major concern for palaeontologists and evolutionary biologists, only a few recent studies have successfully determined the factors that affect niche evolution. Here, we compare the evolution of climatic niches in four main groups of terrestrial vertebrates using a modelling approach integrating both palaeontological and neontological data, and large-scale datasets that contain information on the current distributions, phylogenetic relationships and fossil records for a total of 11,465 species. By reconstructing historical shifts in geographical ranges and climatic niches, we show that niche shifts are significantly faster in endotherms (birds and mammals) than in ectotherms (squamates and amphibians). We further demonstrate that the diversity patterns of the four clades are directly affected by the rate of niche evolution, with fewer latitudinal shifts in ectotherms.

Summary Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. 2. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. 3. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth–death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. 4. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at http://sourceforge.net/projects/pyrate/.

The saxicolous genus Orthophytum (∼60 species, Bromeliaceae) is endemic to eastern Brazil and diversified in xeric habitats of the Atlantic Rainforest, Caatinga and campos rupestres. Within the genus, two main groups are discerned based on the presence or absence of a pedunculate inflorescence, which are further subdivided into several morphological subgroups. However, these systematic hypotheses have not yet been tested in a molecular phylogenetic framework. Here we present the first phylogenetic analysis of Orthophytum using nuclear and plastid markers (phytochrome C, and trnH-psbA and trnL-trnF spacers). Forty species representing the two main groups and all subgroups of Orthophytum, and the related genera Cryptanthus (8 spp.) and Lapanthus (2 spp.) were analyzed. The phylogenetic reconstruction revealed a well-supported clade termed Eu-Orthophytum, containing species with pedunculate inflorescences only. The Orthophytum species with sessile inflorescence formed two clades: (1) the amoenum group and (2) the vagans group plus O. foliosum, the only pedunculate Orthophytum species found outside Eu-Orthophytum. The vagans clade is in sister group position to Eu-Orthophytum. Within the latter, the subgroup mello-barretoi was sister to the most diversified clade, termed Core Orthophytum. Morphological character state reconstructions of floral characters used in previous taxonomic treatments as key diagnostic characters (penduncle presence, corolla form, and petal appendage form) showed different levels of homoplasy.

The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water-impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank-forming lineages compared to tank-less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.

Changes in vitamin D(3) and its metabolites were investigated following UVB- and heat-treatment in the leaves of Solanum glaucophyllum Desf., Solanum lycopersicum L. and Capsicum annuum L. The analytical method used was a sensitive and selective liquid chromatography electrospray ionisation tandem mass spectrometry (LC-ESI-MS/MS) method including Diels-Alder derivatisation. Vitamin D(3) and 25-hydroxy vitamin D(3) were found in the leaves of all plants after UVB-treatment. S. glaucophyllum had the highest content, 200 ng vitamin D(3)/g dry weight and 31 ng 25-hydroxy vitamin D(3)/g dry weight, and was the only plant that also contained 1,25 dihydroxy vitamin D(3) in both free (32 ng/g dry weight) and glycosylated form (17 ng/g dry weight).

Because body size interacts with many fundamental biological properties ofa species, body size evolution can be an essential component of the generationand maintenance of biodiversity. Here we investigate how body sizeevolution can be linked to the clade-specific diversification dynamics indifferent geographical regions. We analyse an extensive body size datasetof Neogene large herbivores (covering approx. 50% of the 970 species inthe orders Artiodactyla and Perissodactyla) in Europe and North Americain a Bayesian framework. We reconstruct the temporal patterns of bodysize in each order on each continent independently, and find significantincreases of minimum size in three of the continental assemblages (exceptEuropean perissodactyls), suggesting an active selection for larger bodies.Assessment of trait-correlated birth-death models indicates that thecommon trend of body size increase is generated by different processes indifferent clades and regions. Larger-bodied artiodactyl species on both continentstend to have higher origination rates, and both clades in NorthAmerica show strong links between large bodies and low extinction rate.Collectively, our results suggest a strong role of species selection and perhapsof higher-taxon sorting in driving body size evolution, and highlightthe value of investigating evolutionary processes in a biogeographic context.

• The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.• We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.• We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.• Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.

Strepsirhines comprise 10 living or recently extinct families, ≥50% of extant primate families. Their phylogenetic relationships have been intensively studied, but common topologies have only recently emerged; e.g. all recent reconstructions link the Lepilemuridae and Cheirogaleidae. The position of the indriids, however, remains uncertain, and molecular studies have placed them as the sister to every clade except Daubentonia, the preferred sister group of morphologists. The node subtending Afro-Asian lorisids has been similarly elusive. We probed these phylogenetic inconsistencies using a test data set including 20 strepsirhine taxa and 2 outgroups represented by 3,543 mtDNA base pairs, and 43 selected morphological characters, subjecting the data to maximum parsimony, maximum likelihood and Bayesian inference analyses, and reconstructing topology and node ages jointly from the molecular data using relaxed molecular clock analyses. Our permutations yielded compatible but not identical evolutionary histories, and currently popular techniques seem unable to deal adequately with morphological data. We investigated the influence of morphological characters on tree topologies, and examined the effect of taxon sampling in two experiments: (1) we removed the molecular data only for 5 endangered Malagasy taxa to simulate ‘extinction leaving a fossil record'; (2) we removed both the sequence and morphological data for these taxa. Topologies were affected more by the inclusion of morphological data only, indicating that palaeontological studies that involve inserting a partial morphological data set into a combined data matrix of extant species should be interpreted with caution. The gap of approximately 10 million years between the daubentoniid divergence and those of the other Malagasy families deserves more study. The apparently contemporaneous divergence of African and non-daubentoniid Malagasy families 40-30 million years ago may be related to regional plume-induced uplift followed by a global period of cooling and drying.

The end of the Pliocene marked the beginning of a period of great climatic variability and sea-level oscillations. Here, based on a new analysis of the fossil record, we identify a previously unrecognized extinction event among marine megafauna (mammals, seabirds, turtles and sharks) during this time, with extinction rates three times higher than in the rest of the Cenozoic, and with 36% of Pliocene genera failing to survive into the Pleistocene. To gauge the potential consequences of this event for ecosystem functioning, we evaluate its impacts on functional diversity, focusing on the 86% of the megafauna genera that are associated with coastal habitats. Seven (14%) coastal functional entities (unique trait combinations) disappeared, along with 17% of functional richness (volume of the functional space). The origination of new genera during the Pleistocene created new functional entities and contributed to a functional shift of 21%, but minimally compensated for the functional space lost. Reconstructions show that from the late Pliocene onwards, the global area of the neritic zone significantly diminished and exhibited amplified fluctuations. We hypothesize that the abrupt loss of productive coastal habitats, potentially acting alongside oceanographic alterations, was a key extinction driver. The importance of area loss is supported by model analyses showing that animals with high energy requirements (homeotherms) were more susceptible to extinction. The extinction event we uncover here demonstrates that marine megafauna were more vulnerable to global environmental changes in the recent geological past than previously thought. The Pliocene marine megafaunal extinctions caused functional diversity loss, which was not mitigated by newly evolved taxa in the Pleistocene. This paper points towards an abrupt loss of productive coastal habitats as a key extinction driver.

Metabolite channeling by a dynamic metabolon The specialized metabolite dhurrin breaks down into cyanide when plant cell walls have been chewed, deterring insect pests. Laursen et al. found that the enzymes that synthesize dhurrin in sorghum assemble as a metabolon in lipid membranes (see the Perspective by Dsatmaichi and Facchini). The dynamic nature of metabolon assembly and disassembly provides dhurrin on an as-needed basis. Membrane-anchored cytochrome P450s cooperated with a soluble glucosyltransferase to channel intermediates toward efficient dhurrin production. Science , this issue p. 890 ; see also p. 829

Dyckia is a xeromorphic bromeliad genus with 168 species distributed throughout south-eastern South America, with the centre of diversity in Brazil. Previous phylogenetic studies based on sequence data revealed, in general, poor resolution among species. To improve our understanding of infrageneric relationships, here we present a molecular phylogenetic analysis of Dyckia based on amplified fragment length polymorphism (AFLP) markers. We also discuss the evolution of floral characters and their implications for the life-history of the genus. Dyckia proved to be well supported as a monophyletic group, although showing a poor resolution in the backbone of the tree. In accordance with previous data, our results suggest that hybridization and introgression have played a significant role in the evolution of the genus. However, the AFLP data showed stronger support for terminal nodes. The results provided deeper insights into the infrageneric relationships, the correlation between species groups, morphological aspects and geographical distribution. Additionally, the character reconstruction corroborates the geographical association found, in which a pattern could generally be observed for species stated as early diverging. Analysing the genus at a population level and taxonomic revision are crucial to understanding the evolutionary dynamics of the clade.

Independent evidence from rocks, fossils, and genes converge on a cohesive narrative of isthmus formation in the Pliocene., The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

Animal clades tend to follow a predictable path of waxing and waning during their existence, regardless of their total species richness or geographic coverage. Clades begin small and undifferentiated, then expand to a peak in diversity and range, only to shift into a rarely broken decline towards extinction. While this trajectory is now well documented and broadly recognised, the reasons underlying it remain obscure. In particular, it is unknown why clade extinction is universal and occurs with such surprising regularity. Current explanations for paleontological extinctions call on the growing costs of biological interactions, geological accidents, evolutionary traps, and mass extinctions. While these are effective causes of extinction, they mainly apply to species, not clades. Although mass extinctions is the undeniable cause for the demise of a sizeable number of major taxa, we show here that clades escaping them go extinct because of the widespread tendency of evolution to produce increasingly specialised, sympatric, and geographically restricted species over time.

Correction to: Palgrave Communications (2016) 2, Article number: 16019. doi: 10.1057/palcomms.2016.19; Published 10 May 2016; Updated 7 June 2016 The middle initial “E” was previously omitted from Michael Alfaro’s name in the author list. This has now been added and reads “Michael E Alfaro”. Erik Gjesfjeld and Michael Alfaro were not previously listed as co-corresponding authors as they should have been.

Cryptanthus comprises 72 species endemic to eastern Brazil with a center of diversity in the Atlantic Forest. The majority of the species are threatened due to habitat loss. We reconstructed phylogenetic relationships in Cryptanthus based on amplified fragment length polymorphisms (AFLP) including 48 species and 109 accessions. The Bayesian phylogenetic analysis revealed four major lineages in Cryptanthus and provided further evidence for the paraphyly of subgen. Hoplocryptanthus, while subgenus Cryptanthus was resolved as monophyletic. Monophyly of previously recognized morphological species groups at sectional level could not be confirmed. Based on the phylogenetic reconstruction we inferred the evolution of the sex system in Cryptanthus via maximum likelihood (ML) ancestral character reconstruction. Homoecy, the possession of hermaphrodite flowers only, was reconstructed as the ancestral state in the genus and characterizes three of the four main lineages within Cryptanthus. Andromonoecy, the possession of male and hermaphrodite flowers on the same plant, evolved only once and represents a synapomorphy of the fourth main lineage, C. subgen. Cryptanthus. The ancestral biome analysis reconstructed Cerrado (semiarid scrublands and forests) and campos rupestres (rock fields) as the most likely ancestral biomes for the genus. A shift to the Atlantic Forest biome was reconstructed to have occurred twice, in the ancestor of the first diverging lineage within the genus and in the ancestor of the C. subgen. Cryptanthus clade. A shift to the Caatinga (tropical dryland savanna) and one reversal to Cerrado (campos rupestres - rock fields) was reconstructed to have occurred once, in C. bahianus and C. arelii, respectively. The ancestral biome reconstruction indicates a high degree of niche conservatism within Cryptanthus with rare biome shifts throughout the evolution of the genus. Further, our results imply that the current infrageneric taxonomy of Cryptanthus is problematic and requires revision.

Aim: To reconstruct the spatio-temporal evolution of Fosterella (Bromeliaceae), a genus characterized by a high degree of endemism in the Central Andes, and to account for contemporary patterns of diversity and distribution within the genus. Location: Fosterella has its centre of diversity in the Central Andes (24 species), where it occurs in two major biomes: the Yungas and seasonally dry tropical forests (SDTF). The genus displays three major disjunctions: Amazonia (one species), Central America (one species), and the Brazilian Shield (five species). Methods: Phylogenetic relationships within Fosterella were inferred based on six plastid DNA regions. Parsimony and likelihood methods, a Bayesian relaxed molecular clock, ancestral area reconstructions, and diversification rate analyses were used to infer the spatio-temporal evolution of Fosterella. Results: The origin of extant lineages of Fosterella was placed in the late Miocene (c. 9.6Ma) during the last rapid Andean uplift. SDTF and azonal lowland sites were inferred as the most likely ancestral habitats. The Yungas were colonized several times independently from c. 4.7Ma onwards. Only one clade diversified in the Yungas, indicative of an ecological shift to moister and cooler conditions. Two recent long-distance dispersals to Central America and to Amazonia were inferred. Diversification rates within Fosterella were found to be constant through time and comparatively low (0.4 species Myr⁻¹). Main conclusions: Allopatric speciation is the main mode of diversification in Fosterella. The isolated distribution of suitable habitats fostered the evolution of a high degree of endemism. The low speciation rates in Fosterella contrast with high diversification rates of Andean high-elevation taxa but are similar to other Andean low- to mid-elevation taxa. The last rapid Andean uplift did not leave a detectable signature in the diversification rates of Fosterella.

Some plant species are known to cause calcium intoxification in grazing animals. This has been attributed to the presence of vitamin D3-like activity. However, research into the presence of vitamin D3 in plants has been limited. One reason for this may be limitations in the analytical methods available for unambiguous detection and quantification of vitamin D3. This paper presents a new method for determining vitamin D3 and its sterol precursors. The method is based on saponification and extraction followed by solid phase clean-up of the compounds from plant leaves and detection by APCI-MS. Recoveries ranged from 101% to 114% and precision from 3% to 12%. Detection limits were 2–8 ng/g fresh weight for the substances tested. In a pilot study we found that Solanum glaucohyllum Desf. and Solanum lycopersicum L. produced vitamin D3 after UV-treatment. The preliminary results presented suggest that vitamin D3 formation in plants is dependent on light exposure.

To search for cytogenetic signatures that can help to clarify evolutionary affinities among the five orders within the Euarchontoglires clade, we focused on associations of conserved syntenic blocks that have been accumulated in the karyotypes of Primates (Strepsirhini and Haplorhini), five families of Rodentia, Scandentia (Tupaia belangeri), Dermoptera (Galeopterus variegatus) and Lagomorpha (Oryctolagus cuniculus). We examined available chromosome painting data to identify conserved chromosomes and chromosomal segments, and syntenic associations likely to have characterized the ancestral eutherian karyotype. The data set includes 161 characters that have been subjected to a concatenated analysis using maximum parsimony (MP) and Bayesian inference (BI). The phylogenetic pattern recovered is generally consistent with reconstructions based on molecular and morphological data (particularly with respect to higher systematic groupings), but there are several anomalies (e.g., in the position of the lagomorphs). Both MP and BI topologies have weak statistical support, as a consequence of the high number of autapomorphic and homoplastic character states that have evolved during the history of the clade. The vast majority of derived associations are located on the terminal portions of the branches, and very few can be identified to support deeper divergences in the tree, indicating that chromosomal structures are far more fluid that was previously recognized. The high levels of homoplasy reflected in our data suggest that the number of possible syntenic character states is limited by chromosomal structures, and the same associations occur repeatedly.

The emergence of the Isthmus of Panama left a major imprint on the biodiversity of the Americas. The connection between South and North America facilitated dispersal of terrestrial and freshwater organisms, while separating marine species between the eastern Pacific and Caribbean seas. Recent geological data have questioned the long-standing view of a Pliocene emergence of the Isthmus (1) and show that the Central American Seaway, defined as the deep oceanic seaway along the tectonic boundary of the South American plate and Panama arc, was already closed by 15–13 Ma (2). Caribbean–Pacific shallow water exchange probably continued, albeit intermittently, until a full closure at 3.5 Ma (1–3). Recently Bacon et al. (3) used molecular and fossil data to evaluate the timing, tempo, and directionality of biotic exchange and vicariance across the Isthmus, and tested whether biological data are congruent with recent geological evidence. Significant increases in terrestrial dispersals were found at ca. 20 and 6 Ma, and increases in marine vicariance at ca. 23 and 7 Ma. Similar patterns prevailed despite intrinsic differences among the taxonomic groups surveyed. This led Bacon et al. (3) to reject the assumption of a single closure of the Isthmus at ca. 3.5 Ma in favor of an older, more complex model of land emergence and biotic interchange.

Cyanogenic glycosides are phytoanticipins involved in plant defence against herbivores by virtue of their ability to release toxic hydrogen cyanide (HCN) upon tissue disruption. In addition, endogenous turnover of cyanogenic glycosides without the liberation of HCN may offer plants an important source of reduced nitrogen at specific developmental stages. To investigate the presence of putative turnover products of cyanogenic glycosides, comparative metabolic profiling using LC–MS/MS and high resolution MS (HR–MS) complemented by ion-mobility MS was carried out in three cyanogenic plant species: cassava, almond and sorghum. In total, the endogenous formation of 36 different chemical structures related to the cyanogenic glucosides linamarin, lotaustralin, prunasin, amygdalin and dhurrin was discovered, including di- and tri-glycosides derived from these compounds. The relative abundance of the compounds was assessed in different tissues and developmental stages. Based on results common to the three phylogenetically unrelated species, a potential recycling endogenous turnover pathway for cyanogenic glycosides is described in which reduced nitrogen and carbon are recovered for primary metabolism without the liberation of free HCN. Glycosides of amides, carboxylic acids and ‘anitriles’ derived from cyanogenic glycosides appear as common intermediates in this pathway and may also have individual functions in the plant. The recycling of cyanogenic glycosides and the biological significance of the presence of the turnover products in cyanogenic plants open entirely new insights into the multiplicity of biological roles cyanogenic glycosides may play in plants.

The history of biodiversity is characterized by a continual replacement of branches in the tree of life. The rise and demise of these branches (clades) are ultimately determined by changes in speciation and extinction rates, often interpreted as a response to varying abiotic and biotic factors. However, understanding the relative importance of these factors remains a major challenge in evolutionary biology. Here we analyze the rich North American fossil record of the dog family Canidae and of other carnivores to tease apart the roles of competition, body size evolution, and climate change on the sequential replacement of three canid subfamilies (two of which have gone extinct). We develop a novel Bayesian analytic framework to show that competition from multiple carnivore clades successively drove the demise and replacement of the two extinct canid subfamilies by increasing their extinction rates and suppressing their speciation. Competitive effects have likely come from ecologically similar species from both canid and felid clades. These results imply that competition among entire clades, generally considered a rare process, can play a more substantial role than climate change and body size evolution in determining the sequential rise and decline of clades.

With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/ .

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space and time constitutes a major scientific challenge in evolutionary biology. With rapidly accumulating species occurrence data, there is an increasing ne ed for making the process of coding species into operational units for biogeographic and evolutionary analyses faster, automated, transparent and reproducible. Here we present SpeciesGeoCoder, a free software package written in Python and R, that allows fo r easy coding of species into user-defined areas. These areas may be of any size and be purely geographical (i.e., polygons) such as political units, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include al titudinal ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurr ence data. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and NEXUS files that can be directly used in many phylogeny-based applications for ancestral state reconstruction, investiga tions on biome evolution, and diversification rate analyses. Our simulations indicate that even datasets containing hundreds of millions of records can be analysed in relatively short time using a regular desktop computer. We exemplify the use of our progr am through two contrasting examples: i) inferring historical dispersal of birds across the Isthmus of Panama, separating lowland vs. montane species and optimising the results onto a species-level, dated phylogeny; and ii) exploring seasonal variations in the occurrence of 10 GPS-tracked individuals of moose (Alces alces) over one year in northern Sweden. These analyses show that SpeciesGeoCoder allows an easy, flexible and fast categorisation of species distribution data for various analyses in ecology and evolution, with potential use at different spatial, taxonomic and temporal scales.

Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.

Sterol uptake in fungi is a multistep process that involves interaction between external sterols and the cell wall, incorporation of sterol molecules into the plasma membrane, and subsequent integration into intracellular membranes for turnover. ATP-binding cassette (ABC) transporters have been implicated in sterol uptake, but key features of their activity remain to be elucidated. Here, we apply fluorescent cholesterol (NBD-cholesterol) to monitor sterol uptake under anaerobic and aerobic conditions in two fungal species, Candida glabrata (Cg) and Saccharomyces cerevisiae (Sc). We found that in both fungal species, ABC transporter-dependent uptake of cholesterol under anaerobic conditions and in mutants lacking HEM1 gene is promoted in the presence of the serum protein albumin that is able to bind the sterol molecule. Furthermore, the C. glabrata ABC transporter CgAus1p expressed in S. cerevisiae requires the presence of serum or albumin for efficient cholesterol uptake. These results suggest that albumin can serve as sterol donor in ABC transporter-dependent sterol uptake, a process potentially important for growth of C. glabrata inside infected humans.

The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.(BDMCMC; biodiversity trends; Birth-death process; incomplete fossil sampling; macroevolution; species rise and fall.)

Aim Small body size in Madagascar’s dwarf and mouse lemurs (Cheirogalei-dae) is generally viewed as primitive. We investigated the evolution of bodysize in this family and in its sister-taxon, the Lepilemuridae, from phylogenetic,ontogenetic and adaptive perspectives.Location Madagascar.Methods We used a phylogenetic method to reconstruct the evolution ofbody size in lemurs, and allometric regression models of gestation periods andstatic and growth allometries in Cheirogaleidae and Lepilemuridae to test thehypothesis that dwarfing occurred as a result of truncated ontogeny (progene-sis). We also examined adaptive hypotheses relating body size to environmentalvariability, life history, seasonality of reproduction, hypothermy (use of tor-por), and a diet rich in plant exudates.Results Our results indicated that cheirogaleids experienced at least four inde-pendent events of body size reduction from an ancestor as large as livingLepilemuridae, by means of progenesis. Our interpretation is supported by thepaedomorphic appearance and parallel ontogenetic trajectories of the dwarftaxa, as well as their very short gestation periods and increased fecundity.Lepilemur species that occupy more predictable environments are significantlylarger than those occupying unpredictable habitats.Main conclusions Cheirogaleidae appear to be paedomorphic dwarfs, a con-sequence of progenesis, probably as an adaptation to high environmentalunpredictability. Although the capacity to use hypothermy is related to smallbody size, this advantage is unlikely to have driven dwarfing in cheirogaleids.We propose that gummmivory/exudativory co-evolved with body size reduc-tion in this clade, probably from a folivorous ancestor. Their small size isderived, and their suitability as models for the ‘ancestral primate’ is thereforedubious.KeywordsAncestor reconstruction, body size evolution, dwarfism, hypervariability,island rule, lemurs, Lepilemuridae, Madagascar, ontogeny, progenesis.INTRODUCTIONThe currently popular model of a small, nocturnal primateancestor was largely inspired by an extant family of Malagasylemurs, the Cheirogaleidae, which includes the smallest livingprimates (30–400 g). Mouse lemurs (Microcebus spp.), inparticular, are believed to have retained a series of primitivecharacters associated with their very small size (30–100 g):nocturnality, insectivorous/omnivorous diet, fast life history,nest-building, altricial infants carried by mouth, solitarysocial structure, and a promiscuous mating system (Charles-Dominique & Martin, 1970; Cartmill, 1972, 1974, 1992;Martin, 1972, 1990; Kappeler, 1998; Wimmer et al., 2002;Gebo, 2004; Scheumann & Zimmermann, 2008; Montgomeryet al., 2010; but see Soligo, 2006; Masters et al., 2007; Soligo& Martin, 2007). This interpretation is frequently associated

Biogeographia vol. XXX - 2011 (Pubblicato il 23 dicembre 2011) La Biogeografia della Sicilia Pattern filogeografici a confronto in specie paleartiche di Coleotteri Scarabaeoidea ASTRID PIZZO, DANIELE SILVESTRO, MASSIMILIANO DELPERO, PIERO CERVELLA, CLAUDLA PALESTRINI, ANTONIO ROLANDO Dzjmrtimento di Biologia Animale e a’e[[’U0m0, Universita‘ degli studi di Torino, via Accczdemia Albertina I3, I 0123 Torino (Italy); e—mzzz'Z: ast7*z'd.pz'zzo @um'to.it Keywords: historical biogeography, CO1, ITS2, Nested Clade Analysis, Likelihood-based methods. SUMMARY The present study aims to compare the population structures and the phylogeographic patterns of species be- longing to two different paleartic genus of Coleopteta Scarabaeidae (77ypocopris and Om‘/Jop/azzgms.s.), whose dis- tributions largely overlap, but whose ecological requirements are deeply different. We tested if mitochondrial poly- morphisms (COI gene) of three species of the genus Yiypocopris, I zzlpizzz/5 (Hagenbach), Yipyremzeux (Charpentier) and T z1ermzli5(L.) reflect morphological and geographic subspecies previously recognised; results showed high con- sistency between molecular and morphological/ geographical data, suggesting that the subspecies can be considered as independent evolutionary units. An additional analysis performed with the help of a likelihood based method for historical biogeography allowed us to evaluate the relative influence of demographic factors like genic flow or drift in shaping the particular phylogeographic patterns observed. Both nested clade analysis and likelihood—based historical reconstruction suggested that Sicilian population of T pyremzeu: separated from Peninsular populations only recently and this is likely due to vicariance mechanisms. On the contrary, Ont/rap/mgu: t(Z1I7‘ZlS(SCl’1I'Cl)C[') and O. illyriczts (Scopoli) did not show any phylogeograhic pattern using COI, because of very low (0. tzzurus) or com- pletely lacking (O. z'll}IrirzLs) haplorype polymorphism. A feeble and little informative phylgeographic structure was found using sequences from ITS2. An estimate of the time of interspecific divergence in each genus located speciation events in a time- frame pleaceble in Pliocene. Differences between the patterns observed are interpreted in the light of the different ecological requirements of the species of the two genus. INTRODUZIONE Il presente lavoro si propone di confrontare la struttura di popolazione ed i pattern filogeografici di specie appartenenti a due diversi generi di Coleotteri Scarabaeoidea, T73/pocopris e Ont/cop/mgus (s.s.), che realizzano corologicamen— te areali in larga parte sovrapposti. ll genere Trypocopris comprende sei specie coprofaghe tipiche di pascoli e fo— reste di media ed alta quota: T alpinus (Hagenbach), T azmedei (Fairrnaire), T pyremzeus (Charpentier), T 7/ermzlis (Linnaeus), Tfitlgidus (Motschulsky) e T

The male gonopores, male reproductive apparatus, spermatophore and spermatozoa of the Mediterranean hermit crab Paguristes eremita are described, using interference phase microscopy, scanning electron microscopy and transmission electron microscopy. A correlation is made between the gonopore morphology and the different kinds of setae accompanying them, and the reproductive biology of these crabs. Each testes merges into a tubular duct made up of four zones: (1) the collecting tubule with free spermatozoa; (2) the proximal zone, where the ampulla of the spermatophores starts to be formed; (3) the medial zone, where the ampulla is completed, the stalk lengthens and the pedestal is formed; (4) the distal zone, where the mature spermatophores are stored. The sizes of the different parts of the spermatophore and of the sperm are given and their exterior morphology and ultrastructure described and compared to congeners. The morphology of the gonopore, male reproductive system, spermatophore and spermatozoa of P. eremita are species-specific, clearly distinguishing the species from the other members of the family. The available spermatozoal and spermatophore data is used to place P. eremita within a sperm phylogeny of the hermit crab family Diogenidae.

Blogeographia vol. XX/X - 2008 (Pubblicato il 30 dicembre 2008) The Mediterranean-southern African disjunct distribution pattern Assessing relationships between Mediterranean and Afrotropical taxa of Cleonini (Coleoptera: Curculionidae: Lixinae): a survey based on Bayesian analysis and lineage geohistory reconstruction MASSIMO MEREGALLI, DANIELE SILVESTRO Dzjnzrtiiizmto 512' Bio/ogizz Animzzle .9 ale//’U0m0, Um'1/erszriz di Torino 2/in Amza'e772ia A/bertzizzz 13, 10123 T072320 (Italy) e—mzzz'[: 77znr5in2o. meregzz[li@zim't0. it Key words: Curculionidae, Cleonini, African Fauna, Mediterranean Fauna, phylogenetic relationships, Bayesian analysis, historical biogeography. SUMMARY Relationships between the Mediterranean and southern African genera oFCleonini (Curculionidae) were assessed using preliminary phylogenetic analysis and palaeohistorical reconstruction by maximum likelihood inference of ancestral distributions. Intergeneric relationships were found to be present only between sister taxa belonging to basal branches of the trees, suggesting that the faunas of the two regions were connected only during the early stages of radiation ofthe tribe. A critical revision ofthe species composition ofsome Afro—Mediterranean genera revealed that only Pram/oremizoriiyinzir has a disjunct Mediterranean—southern African distribution. This is regarded as having been determined by a recent expansion of the range of the genus from the Mediterranean region towards southern Africa via the eastern Africa grasslands. INTRODUCTION The Curculionidae subfamily Lixinae Schoenherr, 1823 is composed of about 100 genera, presently included in three tribes: Lixini Schoenherr, 1823; Rhinocyllini Lacordaire, 1863; and Cleonini Schoenherr, 1826. This last tribe accounts for most of the genera, more than 80. Its taxonomy is still based on Faust (1904), who also provided the only available key to all the genera. Lacking any comprehensive and comparative evaluation of characters, genera are not always clear and unequivocal; in some cases they seem to be para- phyletic taxa, with uncertain boundaries. A phylogenetic analysis of the tribe

The spermatophore morphology and spermatozoal ultrastructure of Diogenes pugilator are described. The spermatophore is typically tripartite made up of an ampulla, a very long stalk and a foot. The two halves making up the ampulla meet at a lateral ridge. The sperm is ovoidal in shape and composed of a large, almost cylindrical, acrosome, which occupies most of the cell volume, capped by a conical operculum, and cupped posteriorly by a cytoplasmic region comprising the nucleus and three arms. The sizes of the different parts of the spermatophore and of the sperm are given and their exterior morphology and ultrastructure described and compared to congeners. The available spermatozoal and spermatophore data is used to place D. pugilator within a sperm phylogeny of the hermit crab family Diogenidae.

The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii . At this stage, Staphylococcaceae ( Jeotgalicoccus and Staphylococcus ) and Lactobacillales ( Aerococcus , Lactobacillus , and Weissella ) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli ( Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales ( Corynebacterium and Yania ) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.

The Italian cigar manufacturing process includes a fermentation step that leads to accumulation of nitrite and tobacco-specific nitrosamines (TSNA), undesirable by-products due to their negative impact on health. In this study, growth and biochemical properties of Debaryomyces hansenii TOB-Y7, a yeast strain that predominates during the early phase of fermentation, have been investigated. With respect to other D. hansenii collection strains (Y7426, J26, and CBS 1796), TOB-Y7 was characterized by the ability to tolerate very high nitrite levels and to utilize nitrite, but not nitrate, as a sole nitrogen source in a chemically defined medium, a property that was enhanced in microaerophilic environment. The ability to assimilate nitrite was associated to the presence of YNI1, the gene encoding the assimilatory NAD(P)H:nitrite reductase (NiR), absent in Y7426, J26, and CBS 1796 by Southern blot data. YNI1 from TOB-Y7 was entirely sequenced, and its expression was analyzed in different media by Northern blot and reverse transcriptase polymerase chain reaction. The evidence that, in D. hansenii TOB-Y7, YNI1 was transcriptional active also in the presence of high ammonia concentration typical of tobacco fermentation, stimulated the development of an improved process that, on a laboratory scale, was proved to be effective in minimizing nitrite and TSNA accumulation.

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales.

Background Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling.

Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after speciation are samples of a parent population, we can expect their mean phenotypes to randomly differ from one another potentially generating a “jump” of mean phenotypes due to asymmetrical trait inheritance at cladogenesis. Here, we aim to clarify the effect of asymmetrical trait inheritance at speciation on macroevolutionary analyses, focusing on model testing and parameter estimation using some of the most common models of quantitative trait evolution. We developed an individual-based simulation framework in which the evolution of phenotypes is determined by trait changes at the individual level accumulating across generations, and cladogenesis occurs then by separation of subsets of the individuals into new lineages. Through simulations, we assess the magnitude of phenotypic jumps at cladogenesis under different modes of trait inheritance at speciation. We show that even small jumps can strongly alter both the results of model selection and parameter estimations, potentially affecting the biological interpretation of the estimated mode of evolution of a trait. Our results call for caution when interpreting analyses of trait evolution, while highlighting the importance of testing a wide range of alternative models. In the light of our findings, we propose that future methodological advances in comparative methods should more explicitly model the intraspecific variability around species mean phenotypes and how it is inherited at speciation.

Data and scripts associated with the paper. Updated version of the code will be available here:https://github.com/dsilvestro/rootBBB

O objetivo geral desta dissertação é testar hipóteses relacionadas à duração das linhagens (i.e. o intervalo de tempo definido pela origem e extinção das diferentes linhagens) e à dinâmica da diversificação dos ruminantes. Para isso, nós usamos compilações públicas de dados fósseis e modelos probabilísticos. Como a literatura macroevolutiva se aproveita das múltiplas escalas taxonômicas onde é possível estudar a mudança da biodiversidade no tempo, os dois capítulos desta dissertação testam suas hipóteses no níveis de espécie e gênero na tentativa de iluminar o papel da escala na manifestação dos padrões macroevolutivos. No primeiro capítulo, nós investigamos se tratamentos taxonômicos distintos aplicados aos dados brutos alteram os resultados obtidos por um método macroevolutivo. Nossos resultados sugerem que os dados, mesmo após passar por diferentes tratamentos, indicam similares dinâmicas de diversificação tanto no nível taxonômico dos gêneros quanto no nível das espécies. Por outro lado, as comparações entre dois conjuntos de dados inicialmente distintos podem gerar diferenças consideráveis na dinâmica da diversificação e inclusive indicar diferenças entre escalas taxonômicas. Esses resultados são robustos mesmo que as imperfeições do registro fóssil sejam consideradas de diferentes maneiras pelo método usado. No segundo capítulo, nós usamos modelos probabilísticos para testar uma importante hipótese macroevolutiva que é também considerada uma premissa para vários estudos da área: a de que a probabilidade de extinção de qualquer linhagem é independente da sua longevidade, ou seja, do intervalo de tempo que a linhagem já viveu. Nossos resultados sugerem um padrão consistente de diminuição na probabilidade de extinção conforme as espécies vivem por mais tempo, enquanto que o padrão observado do no nível dos gêneros é menos claro. Este resultado não só enriquece o nosso conhecimento a respeito da dinâmica da extinção de linhagens, como sugere que a premissa de independência de idade na probabilidade de extinção (importante para vários estudos macroevolutivos) pode não ser válida, pelo menos para Ruminantia. Nós esperamos que os dados e ideias aqui expostos interajam com novas ideias e dados do leitor, estimulando o desenvolvimento da macroevolução The main goal of this dissertation is to test hypotheses related to the duration of the lineages (i.e. the time interval between the origin and extinction of each lineage) and to the diversification dynamics of the ruminants. To achieve this goal, we used public compilations of fossil data and probabilistic models. As the macroevolutionary literature take advantage of multiple taxonomic scales in which is possible to study biodiversity changes through time, the two chapters of this dissertation tested different hypotheses in both the species and genus levels, as na attempt to shed some light on the role of scale influencing the macroevolutionary phenomena. In the first chapter, we investigated if different taxonomic treatments applied over the raw data significantly change the results obtained from a macroevolutionary method. Our results suggest that the same data, even passing through different data curations, indicate similar diversification dynamics in species and genus taxonomic levels. On the other hand, data that comes from different sources may present considerable differences in the diversification dynamics, and even indicate differences between taxonomic scales. These results are robust to different considerations of the preservation biases of the fossil record by the method. In the second chapter, we used probabilistic models to test an importante macroevolutionary hypothesis that is also considered a premise of several macroevolutionary studies: that the probability of extinction of any lineage is independent of its longevity (the time span determined by the origination and extinction of each lineage). Our results suggest a consistent pattern of decreasing extinction probability as species live for longs periods of time, but the pattern presented by the genera is less clear. These results not only enhance our knowledge about extinction dynamics, but it also suggests that the premise of age independence in the extinction probability (important for several macroevolutionary studies) might not be valid, at least for Ruminatia. We hope our data and ideas interact with new ideas and data from the reader to stimulate the development of the macroevolutionary field