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The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we investigated the evolution, taxonomic diversity and morphological disparity of Nitraria throughout the Cenozoic by integrating extant taxa and fossil palynological morphotypes into a unified phylogenetic framework based on both DNA sequences and pollen morphological data. We present the oldest fossil pollen grain of Nitraria, at least 53 Myr old. This fossil was found in Central Asian deposits, providing new evidence for its origin in this area. We found that the EOT is an evolutionary bottleneck for Nitraria, coinciding with retreat of the proto-Paratethys Sea, a major global cooling event and a turnover in Central Asian steppe vegetation. We infer the crown age of modern Nitraria spp. to be significantly younger (Miocene) than previously estimated (Palaeocene). The diversity trajectory of Nitraria inferred from extant-only taxa differs markedly from one that also considers extinct taxa. Our study demonstrates it is therefore critical to apply an integrative approach to fully understand the plant evolutionary history of Nitrariaceae.

AimThe global Red List (RL) from the International Union for the Conservation of Nature is the most comprehensive global quantification of extinction risk, and widely used in applied conservation as well as in biogeographic and ecological research. Yet, due to the time- consuming assessment process, the RL is biased taxonomically and geographically, which limits its application on large scales, in particular for understudied areas such as the tropics, or understudied taxa, such as most plants and invertebrates. Here we present IUCNN, an R- package implementing deep learning models to predict species RL status from publicly available geographic occurrence records (and other traits if available).InnovationWe implement a user-friendly workflow to train and validate neural network models, and subsequently use them to predict species RL status. IUCNN contains functions to address specific issues related to the RL framework, including a regression-based approach to account for the ordinal nature of RL categories and class imbalance in the training data, a Bayesian approach for improved uncertainty quantification, and a target accuracy threshold approach that limits predictions to only those species whose RL status can be predicted with high confidence. Most analyses can be run with few lines of code, without prior knowledge of neural network models. We demonstrate the use of IUCNN on an empirical dataset of ∼14,000 orchid species, for which IUCNN models can predict extinction risk within minutes, while outperforming comparable methods.Main conclusionsIUCNN harnesses innovative methodology to estimate the RL status of large numbers of species. By providing estimates of the number and identity of threatened species in custom geographic or taxonomic datasets, IUCNN enables large-scale analyses on the extinction risk of species so far not well represented on the official RL.

Aim: Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (www.bio-dem.surge.sh), an open-source software to explore the relationship between the availability of species occurrence records and the political framework in countries worldwide and through time. Location: Global. Taxon: Any. Methods: Bio-Dem accesses the number of occurrence records available from countries worldwide from the Global Biodiversity Information Facility (www.gbif.org) and socio-political information from these countries from the Varieties of Democracy database (www.v-dem.net) as well as information on colonial history from the Issue Correlates of War Project. Results: Bio-Dem is available as a free graphical user interface web application at www.bio-dem.surge.sh. Through three interactive graphs, Bio-Dem enables users to explore the relationship between species occurrence records and countries’ regime type, freedom of movement, freedom of association, gross domestic product, education length, political corruption, armed conflict and colonial history. We describe possible links of these specific political indicators with the collection and mobilization of biodiversity data. Illustrative examples and video tutorials explaining the use of Bio-Dem are available at www.bio-dem.surge.sh. Main conclusions: Bio-Dem provides a user-friendly way to explore the link between socio-political variables and the availability of species occurrence records in user-selected taxa and geographic regions, and to generate hypotheses on their connection. We envision Bio-Dem as a useful tool for teachers communicating the caveats of available biodiversity data, for biodiversity scientists exploring potential spatial and temporal bias in their data, and for social scientists exploring the impact of political systems on scientific data collection and biodiversity conservation.

The ongoing environmental crisis poses an urgent need to forecast the who, where and when of future species extinctions, as such information is crucial for targeting conservation efforts. Commonly, such forecasts are made based on conservation status assessments produced by the International Union for Conservation of Nature (IUCN). However, when researchers apply these IUCN conservation status data for predicting future extinctions, important information is often omitted, which can impact the accuracy of these predictions. Here we present a new approach and a software for simulating future extinctions based on IUCN conservation status information, which incorporates generation length information of individual species when modeling extinction risks. Additionally, we explicitly model future changes in conservation status for each species, based on status transition rates that we estimate from the IUCN assessment history of the last decades. Finally, we apply a Markov chain Monte Carlo algorithm to estimate extinction rates for each species, based on the simulated future extinctions. These estimates inherently incorporate the chances of conservation status changes and the generation length for each given species and are specific to the simulated time frame. We demonstrate the utility of our approach by estimating future extinction rates for all bird species. Our average extinction rate estimate for the next 100 yr across all birds is 6.98 x 10(-4) extinctions per species-year, and we predict an expected biodiversity loss of between 669 and 738 bird species within that time frame. Further, the rate estimates between species sharing the same IUCN status show larger variation than the rates estimated with alternative approaches, which reflects expected differences in extinction risk among taxa of the same conservation status. Our method demonstrates the utility of applying species-specific information to the estimation of extinction rates, rather than assuming equal extinction risks for species assigned to the same conservation status.

International Union for Conservation of Nature (IUCN) Red List assessments are essential for prioritizing conservation needs but are resource intensive and therefore available only for a fraction of global species richness. Automated conservation assessments based on digitally available geographic occurrence records can be a rapid alternative, but it is unclear how reliable these assessments are. We conducted automated conservation assessments for 13,910 species (47.3% of the known species in the family) of the diverse and globally distributed orchid family (Orchidaceae), for which most species (13,049) were previously unassessed by IUCN. We used a novel method based on a deep neural network (IUC-NN). We identified 4,342 orchid species (31.2% of the evaluated species) as possibly threatened with extinction (equivalent to IUCN categories critically endangered [CR], endangered [EN], or vulnerable [VU]) and Madagascar, East Africa, Southeast Asia, and several oceanic islands as priority areas for orchid conservation. Orchidaceae provided a model with which to test the sensitivity of automated assessment methods to problems with data availability, data quality, and geographic sampling bias. The IUC-NN identified possibly threatened species with an accuracy of 84.3%, with significantly lower geographic evaluation bias relative to the IUCN Red List and was robust even when data availability was low and there were geographic errors in the input data. Overall, our results demonstrate that automated assessments have an important role to play in identifying species at the greatest risk of extinction.Evaluación Automatizada de la Conservación de la Familia Orchidaceae mediante Aprendizaje Profundo Resumen Los análisis de la Lista Roja de la Unión Internacional para la Conservación de la Naturaleza (UICN) son esenciales para la priorización de las necesidades de conservación, pero requieren de muchos recursos y por lo tanto están disponibles sólo para una fracción de la riqueza mundial de especies. Las evaluaciones automatizadas de la conservación basadas en los registros disponibles de presencia geográfica pueden ser una alternativa rápida pero no está claro cuán confiables son estas evaluaciones. Realizamos evaluaciones automatizadas de la conservación para 13,910 especies (47.3% de las especies conocidas de la familia) de la diversa y mundialmente distribuida familia de las orquídeas (Orchidaceae), en la cual la mayoría de las especies (13,049) no tenían una valoración previa por parte de la UICN. Usamos un método novedoso basado en una red neural profunda (IUC-NN). Identificamos 4,342 especies de orquídeas (31.2% de las especies evaluadas) como posiblemente amenazadas por la extinción (equivalente a las categorías de la UICN en peligro crítico [CR], en peligro [EN] o vulnerable [VU]) y a Madagascar, África Occidental, el sudeste de Asia y varias islas oceánicas como áreas prioritarias para la conservación de orquídeas. La familia Orchidaceae proporcionó un modelo con el cual probar la sensibilidad de los métodos de evaluación automatizada ante problemas con la disponibilidad de datos, la calidad de los datos y los sesgos de muestreo geográfico. La IUC-NN identificó posibles especies amenazadas con una certeza de 84.3% con un sesgo de evaluación geográfica significativamente más bajo en relación con la Lista Roja de la UICN y mostró solidez incluso cuando la disponibilidad de datos fue baja y hubo errores geográficos en los datos de entrada. En general, nuestros resultados demostraron que las evaluaciones automatizadas tienen un papel importante que desempeñar en la identificación de especies con mayor riesgo de extinción.

Research data are available on the Mendeley Data platform (https://doi.org/10.17632/xfx2yhw949.2), which include datasets, input files and R scripts of the analyses., Appendix A. Supplementary material Supplementary data to this article can be found online at https://doi. org/10.1016/j.ympev.2022.107635, Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates., Portuguese National Funds through FCT (Fundação para a Ciência e a Tecnologia) supported this work with the projects UIDP/50027/2020 and PTDC/BIA-EVL/31254/2017, Contract grant to AC [2020.00823.CEECIND/CP1601/CT0003, PD/BD/128493/2017, SFRH/BD/102495/2014, SFRH/BPD/111015/2015, Agencia Española de Investigación, with a Juan de la Cierva-Formación grant [FCI2019-039443-I/AEI/10.13039/501100011033], Swedish Research Council [2019-05191], Swiss National Science Foundation [PCEFP3_187012], Swedish Research Council [VR: 2019-04739]

Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong support for a Boreotropical origin of the family with contrasting evolutionary trajectories between the temperate subfamily Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae rapidly evolved frost tolerance when the global climate shifted to ice-house conditions from the Oligocene, with diversification at high latitudes especially in Europe and Asia during the Miocene. Subsequent range contraction at high latitudes and high levels of extinction in Europe driven by global cooling led to the current regional disparity in species diversity. Engelhardioideae showed temperature conservatism while adapting to increased humidity, tracking tropical climates to low latitudes since the middle Eocene with comparatively little diversification, perhaps due to high competition in the tropical zone. The biogeographic history of Juglandaceae shows that the North Atlantic land bridge and Europe played more critical roles than previously thought in linking the floras of East Asia and North America, and showcases the complex interplay among climate change, niche evolution, dispersal, and extinction that shaped the modern disjunct pattern of species richness in temperate woody plants. [Boreotropical origin; climatic niche evolution; disjunct distribution; dispersal; diversity anomaly; extinction; Juglandaceae.]

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder ‘Symphyta’, which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the ‘Symphyta’, with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes – and back – have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.

Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin’s hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling. Using a novel Bayesian method, the authors infer a pre-Cretaceous origin for multiple angiosperm families on the basis of their fossil record and present-day diversity.

raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to setup and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML, built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings, and one-click model testing to select the best substitution models using ModelTest-NG. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML-NG, which provides new functionality and higher performance on large datasets. raxmlGUI 2.0 facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.

The pleiotropic drug resistance (PDR) transporter Pdr11p is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae, where it facilitates the uptake of exogenous sterols. Members of the fungal PDR family contain six conserved cysteines in their extracellular loops (ECL). For the functional analysis of these cysteine residues in Pdr11p, we generated a series of single cysteine-to-serine mutants. All mutant proteins expressed well and displayed robust ATPase activity upon purification. Mass-spectrometry analysis identified two cysteine residues (C582 and C603) in ECL3 forming a disulfide bond. Further characterization by cell-based assays showed that all mutants are compromised in facilitating sterol uptake, protein stability, and trafficking to the plasma membrane. Our data highlight the fundamental importance of all six extracellular cysteine residues for the functional integrity of Pdr11p and provide new structural insights into the PDR family of transporters.

Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.

Saber-toothed cats were armed with formidable weapons. They evolved a number of highly derived morphological features, most notably a pair of extremely long upper canines, which makes them unique within the felid family. Although the sabertooth character evolved several times among carnivorous mammals, sabertooth clades mostly had disjunctive occurrences both in space and time, and no sabertooth is alive today. We studied the rates of phenotypic and taxonomic diversification in the mandible of sabertooths, as compared to the rates calculated for both extinct and extant conical toothed cats. We found that the mandible's shape and physical properties in sabertooth clades evolved at distinctly higher rates than the rest of the felid tree. In addition, sabertooths had similar speciation rate to conical toothed cats, but statistically higher extinction rate. The wealth of morphological specializations required to be a sabertooth, and their tendency to focus on large-sized species as prey, was likely responsible for such high extinction rate, and for the peculiar, disjunctive patterns of sabertooth clade occurrence in the fossil record. © 2018 Elsevier B.V.

Linking pattern to process across spatial and temporal scales has been a key goal of the field of biogeography. In January 2017, the 8th biennial conference of the International Biogeography Society sponsored a symposium on Building up biogeography—process to pattern that aimed to review progress towards this goal. Here we present a summary of the symposium, in which we identified promising areas of current research and suggested future research directions. We focus on (1) emerging types of data such as behavioural observations and ancient DNA, (2) how to better incorporate historical data (such as fossils) to move beyond what we term “footprint measures” of past dynamics and (3) the role that novel modelling approaches (e.g. maximum entropy theory of ecology and approximate Bayesian computation) and conceptual frameworks can play in the unification of disciplines. We suggest that the gaps separating pattern and process are shrinking, and that we can better bridge these aspects by considering the dimensions of space and time simultaneously.

A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here, we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within-clade diversity dependence suppressing speciation rates and detected between-clade effects increasing extinction rates in six instances. Diversity dependence often involved lineages that migrated between continents and we found that speciation was more responsive to diversity changes within the clade, whereas extinction responded to diversity of taxa in other clades. The analysis of the fossil record of Carnivora suggests that interactions within and between clades are associated with different speciation and extinction regimes, opening room for a broader theory of diversity dependence.

International audience; Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long timescales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence for the impact of interactions on macroevolutionary patterns of trait evolution and diversification, yet many macroevolutionary studies have only a tenuous relationship to ecological studies of interactions over shorter timescales. We review current research in this area, highlighting approaches that explicitly model species interactions and connect them to broad-scale macroevolutionary patterns. We also suggest that progress has been made by taking an integrative interdisciplinary look at individual clades. We focus on African cichlids as a case study of how this approach can be fruitful. Overall, although the evidence for species interactions shaping macroevolution is strong, further work using integrative and model-based approaches is needed to spur progress towards understanding the complex dynamics that structure communities over time and space.

New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5-10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small-weighing 0.4 kg-and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends. Fil: Silvestro, Daniele. University Goteborg; Suecia. Universite de Lausanne; Suiza. Gothenburg Global Biodiversity Center; Suecia. Swiss Institute of Bioinformatics; Suiza Fil: Tejedor, Marcelo Fabian. University Goteborg; Suecia. Gothenburg Global Biodiversity Center; Suecia. Swiss Institute of Bioinformatics; Suiza. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Geología y Paleontología; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; Argentina Fil: Serrano Serrano, Martha L.. Universite de Lausanne; Suiza Fil: Loiseau, Oriane. Universite de Lausanne; Suiza. Swiss Institute of Bioinformatics; Suiza Fil: Rossier, Victor. Universite de Lausanne; Suiza. Swiss Institute of Bioinformatics; Suiza Fil: Rolland, Jonathan. Universite de Lausanne; Suiza. University of British Columbia; Canadá Fil: Zizka, Alexander. University Goteborg; Suecia. Gothenburg Global Biodiversity Center; Suecia Fil: Höhna, Sebastian. Ludwig Maximilians Universitat; Alemania Fil: Antonelli, Alexandre. University Goteborg; Suecia. Gothenburg Global Biodiversity Center; Suecia. Harvard University; Estados Unidos. Gothenburg Botanical Garden; Suecia Fil: Salamin, Nicolas. Universite de Lausanne; Suiza. Swiss Institute of Bioinformatics; Suiza

The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabelling encountered when searching for suitable sequences for phylogenetic analysis. These issues include the incorrect identification of sequenced species, non-standardised and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users, among others. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR, that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.

The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the only direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time. The software PyRate implements a Bayesian framework to analyze fossil occurrence data to estimate the rates of preservation, origination, and extinction while incorporating several sources of uncertainty. Building upon this framework, we present a suite of methodological advances including more complex and realistic models of preservation and the first likelihood-based test to compare the fit across different models. Further, we develop a new reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, which provides more reliable results and includes an explicit estimation of the number and temporal placement of statistically significant rate changes. Finally, we implement a new C++ library that speeds up the analyses by orders of magnitude, therefore facilitating the application of the PyRate methods to large data sets. We demonstrate the new functionalities through extensive simulations and with the analysis of a large data set of Cenozoic marine mammals. We compare our analytical framework against two widely used alternative methods to infer origination and extinction rates, revealing that PyRate decisively outperforms them across a range of simulated data sets. Our analyses indicate that explicit statistical model testing, which is often neglected in fossil-based macroevolutionary analyses, is crucial to obtain accurate and robust results.

The evolution of organisms is crucially dependent on the evolution of intraspecific variation. Its interactions with selective agents in the biotic and abiotic environments underlie many processes, such as intraspecific competition, resource partitioning and, eventually, species formation. Nevertheless, comparative models of trait evolution neither allow explicit testing of hypotheses related to the evolution of intraspecific variation nor do they simultaneously estimate rates of trait evolution by accounting for both trait mean and variance. Here, we present a model of phenotypic trait evolution using a hierarchical Bayesian approach that simultaneously incorporates interspecific and intraspecific variation. We assume that species-specific trait means evolve under a simple Brownian motion process, whereas species-specific trait variances are modeled with Brownian or Ornstein-Uhlenbeck processes. After evaluating the power of the method through simulations, we examine whether life-history traits impact evolution of intraspecific variation in the Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily extendible to more complex scenarios of the evolution of inter- and intraspecific variation and presents a step toward more comprehensive comparative models for macroevolutionary studies.

In the version of this Article originally published, in Fig. 3a the first boundary was incorrectly labelled the “K/T boundary”; it should have read the “K/Pg boundary”. The two equations in the main text were incorrectly omitted from the HTML. In the description of the posterior distribution of an ancestral state, the normal distribution was incorrectly described as being “assigned as prior to the node value”; it should have read “assigned as calibration to the node value”. In the associated equation (the second equation in the text), the denominator of the last term was incorrectly given as “Node prior”; it should have read “Node calibration”. In the same equation, the numerator of the third term on the right-hand side of the equation contained incorrect superscript notation on the x and this is shown in the full equation in the notice below. In the Acknowledgements, the following two sentences were incorrectly omitted: “The authors thank the Vital-IT facilities of the Swiss Institute of Bioinformatics for the computational support” and “This work was funded by the University of Lausanne and the Swiss National Science Foundation (CRSIII3-147630) to N.S.” In the Author contributions section, the first sentence was incorrectly given as “J.R. designed the study. J.R., N.S. and D. Silvestro designed the methodology and ran the analyses”; it should have read “J.R., D.S. and N.S. designed the study and the methodology”. In the Supplementary Information, all three instances of the word “prior” were incorrect and should have read “calibration”. These errors have now been corrected in all versions of the Article.

Summary The evolution of continuous traits is the central component of comparative analyses in phylogenetics, and the comparison of alternative models of trait evolution has greatly improved our understanding of the mechanisms driving phenotypic differentiation. Several factors influence the comparison of models, and we explore the effects of random errors in trait measurement on the accuracy of model selection. We simulate trait data under a Brownian motion model (BM) and introduce different magnitudes of random measurement error. We then evaluate the resulting statistical support for this model against two alternative models: Ornstein–Uhlenbeck (OU) and accelerating/decelerating rates (ACDC). Our analyses show that even small measurement errors (10%) consistently bias model selection towards erroneous rejection of BM in favour of more parameter-rich models (most frequently the OU model). Fortunately, methods that explicitly incorporate measurement errors in phylogenetic analyses considerably improve the accuracy of model selection. Our results call for caution in interpreting the results of model selection in comparative analyses, especially when complex models garner only modest additional support. Importantly, as measurement errors occur in most trait data sets, we suggest that estimation of measurement errors should always be performed during comparative analysis to reduce chances of misidentification of evolutionary processes.

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.

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.

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.

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.

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.

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/ .

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

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

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.