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The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Background: Mental health difficulties among university students have been rising rapidly over the last decade, and the demand for university mental health services commonly far exceeds available resources. Digital interventions are seen as one potential solution to these challenges. However, as in other mental health contexts, digital programs often face low engagement and uptake, and the field lacks usable, engaging, evidence-supported mental health interventions that may be used flexibly when students need them most., Objective: The aim of this study is to investigate the feasibility and acceptability of a new, in situ intervention tool (Purrble) among university students experiencing anxiety. As an intervention, Purrble was designed to provide in situ support for emotion regulation (ER)-a well-known transdiagnostic construct-directly in the moments when individuals are facing emotionally challenging situations. A secondary aim is to consider the perceived impact of Purrble on youth mental health, as reported by students over a 7-week deployment., Methods: A mixed methods open trial was conducted with 78 under- and postgraduate students at Oxford University. Participants were recruited based on moderate to high levels of anxiety measured by Generalized Anxiety Disorder-7 at baseline (mean 16.09, SD 3.03). All participants had access to Purrble for 7 weeks during the spring term with data on their perceived anxiety, emotion dysregulation, ER self-efficacy, and engagement with the intervention collected at baseline (pre), week 4 (mid), and week 8 (postintervention). Qualitative responses were also collected at the mid- and postintervention points., Results: The findings demonstrated a sustained engagement with Purrble over the 7-week period, with the acceptability further supported by the qualitative data indicating that students accepted Purrble and that Purrble was well-integrated into their daily routines. Exploratory quantitative data analysis indicated that Purrble was associated with reductions in student anxiety (dz=0.96, 95% CI 0.62-1.29) and emotion dysregulation (dz=0.69, 95% CI 0.38-0.99), and with an increase in ER self-efficacy (dz=-0.56, 95% CI -0.86 to -0.26)., Conclusions: This is the first trial of a simple physical intervention that aims to provide ongoing ER support to university students. Both quantitative and qualitative data suggest that Purrble is an acceptable and feasible intervention among students, the engagement with which can be sustained at a stable level across a 7-week period while retaining a perceived benefit for those who use it (n=32, 61% of our sample). The consistency of use is particularly promising given that there was no clinician engagement or further support provided beyond Purrble being delivered to the students. These results show promise for an innovative intervention model, which could be complementary to the existing interventions., (©A Jess Williams, Maureen Freed, Nikki Theofanopoulou, Claudia Daudén Roquet, Predrag Klasnja, James Gross, Jessica Schleider, Petr Slovak. Originally published in JMIR Mental Health (https://mental.jmir.org), 31.10.2023.)

The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium . Consequently, we propose the three new genera Afrocarduus , Afrocirsium and Nuriaea ; the latter did notably not belong to the Carduus - Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization.

The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.

Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single-copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM., (© 2022 John Wiley & Sons Ltd.)

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras., (© 2022. The Author(s).)

Competing Interests: The authors declare no competing interest.

Background: Emotion regulation is a key transdiagnostic risk factor for a range of psychopathologies, making it a prime target for both prevention and treatment interventions in childhood. Existing interventions predominantly rely on workshops or in-person therapy-based approaches, limiting the ability to promote emotion regulation competence for children in everyday settings and at scale. Purrble is a newly developed, inexpensive, socially assistive robot-in the form of an interactive plush toy-that uses haptic feedback to support in-the-moment emotion regulation. It is accessible to children as needed in their daily lives, without the need for a priori training. Although qualitative data from previous studies show high engagement in situ and anecdotal evidence of the robot being incorporated into children's emotion regulation routines, there is no quantitative evidence of the intervention's impact on child outcomes., Objective: The aim of this study is to examine the efficacy of a new intervention model for child-led emotion regulation-Purrble-that can be deployed across prevention and treatment contexts., Methods: Overall, 134 children aged 8 to 10 years will be selected from an enriched nonclinical North American population; for inclusion, the cutoff for the parents' rating of child dysregulation will be ≥10 points in the total difficulties score on the Strengths and Difficulties Questionnaire. This cutoff was selected to obtain a measurable, but not necessarily clinical, level of the child's emotion regulatory difficulties. The selected families will be randomly assigned with .5 probability to receive either a Purrble or an active control (noninteractive plush toy). The primary outcome will be a daily ecological momentary assessment measure of child emotion regulation capability (as reported by parents) over a period of 4 weeks. Exploratory analyses will investigate the intervention impact on secondary outcomes of child emotion regulation, collected weekly over the same 4-week period, with follow-ups at 1 month and 6 months postdeployment. Quantitative data will be analyzed on an intent-to-treat basis. A proportion of families (approximately 30% of the sample) will be interviewed after deployment as part of the process analysis., Results: The study is funded by the UKRI Future Leaders Fellowship (MR/T041897/1) and an in-kind contribution from the Committee for Children. This study received ethical approval from the Pearl institutional review board (#18-CFC-101). Participant recruitment started in February 2021, with the 1-month deployment in April-May 2021. The results of this analysis will be published in 2022., Conclusions: This study will be the first quantitative evaluation of the efficacy of an innovative, proof-of-concept intervention model for an in situ, child-led emotion regulation intervention. Insights into the trajectory of daily changes, complemented with weekly questionnaire batteries and postdeployment interviews, will result in an in-depth understanding of whether and how the hypothesized intervention logic model works, leading to further intervention optimization., Trial Registration: ClinicalTrials.gov NCT04810455; http://clinicaltrials.gov/ct2/show/NCT04810455., International Registered Report Identifier (irrid): PRR1-10.2196/28914., (©Petr Slovak, Brett Q Ford, Sherri Widen, Claudia Daudén Roquet, Nikki Theofanopoulou, James J Gross, Benjamin Hankin, Predrag Klasnja. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 09.11.2021.)

High elevation temperate mountains have long been considered species poor owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-elevation plant clade (Androsace sect. Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. We inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species of Androsace dwelling on different bedrock types on the rooftops of the Alps. This highlights that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.

Background: The regular practice of mindfulness has been shown to provide benefits for mental well-being and prevent depression relapse. Technology-mediated interventions can facilitate the uptake and sustained practice of mindfulness, yet the evaluation of interactive systems, such as brain-computer interfaces, has been little explored., Objective: The objective of this paper is to present an interactive mindfulness-based technology to improve mental well-being in people who have experienced depression. The system, Anima, is a brain-computer interface that augments mandala coloring by providing a generative color palette based on the unfolding mindfulness states during the practice. In addition, this paper outlines a multiple-baseline, single-case experimental design methodology to evaluate training effectiveness., Methods: Adult participants who have experienced depression in the past, have finished treatment within the last year, and can provide informed consent will be able to be recruited. The Anima system, consisting of 2 tablets and a nonintrusive mental activity headband, will be delivered to participants to use during the study. Measures include state and trait mindfulness, depression symptoms, mental well-being, and user experience, and these measures will be taken throughout the baseline, intervention, and monitoring phases. The data collection will take place in the form of a questionnaire before and after each mandala-coloring session and a semistructured interview every 2 weeks. Trial results will be analyzed using structured visual analysis, supplemented with statistical analysis appropriate to single-case methodology., Results: Study results will offer new insights into the deployment and evaluation of novel interactive brain-computer interfaces for mindfulness training in the context of mental health. Moreover, findings will validate the effectiveness of this training protocol to improve the mental well-being of people who have had depression. Participants will be recruited locally through the National Health Service., Conclusions: Evidence will assist in the design and evaluation of brain-computer interfaces and mindfulness technologies for mental well-being and the necessary services to support people who have experienced depression., International Registered Report Identifier (irrid): PRR1-10.2196/20819., (©Claudia Daudén Roquet, Corina Sas. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 18.01.2021.)

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL ) and herbarium material (87% ITS2, 98% matK and rbcL ). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

Background: In the last decade, there has been a proliferation of mobile apps claiming to support the needs of people living with depression. However, it is unclear what functionality is actually provided by apps for depression, or for whom they are intended., Objective: This paper aimed to explore the key features of top-rated apps for depression, including descriptive characteristics, functionality, and ethical concerns, to better inform the design of apps for depression., Methods: We reviewed top-rated iPhone OS (iOS) and Android mobile apps for depression retrieved from app marketplaces in spring 2019. We applied a systematic analysis to review the selected apps, for which data were gathered from the 2 marketplaces and through direct use of the apps. We report an in-depth analysis of app functionality, namely, screening, tracking, and provision of interventions. Of the initially identified 482 apps, 29 apps met the criteria for inclusion in this review. Apps were included if they remained accessible at the moment of evaluation, were offered in mental health-relevant categories, received a review score greater than 4.0 out of 5.0 by more than 100 reviewers, and had depression as a primary target., Results: The analysis revealed that a majority of apps specify the evidence base for their intervention (18/29, 62%), whereas a smaller proportion describes receiving clinical input into their design (12/29, 41%). All the selected apps are rated as suitable for children and adolescents on the marketplace, but 83% (24/29) do not provide a privacy policy consistent with their rating. The findings also show that most apps provide multiple functions. The most commonly implemented functions include provision of interventions (24/29, 83%) either as a digitalized therapeutic intervention or as support for mood expression; tracking (19/29, 66%) of moods, thoughts, or behaviors for supporting the intervention; and screening (9/29, 31%) to inform the decision to use the app and its intervention. Some apps include overtly negative content., Conclusions: Currently available top-ranked apps for depression on the major marketplaces provide diverse functionality to benefit users across a range of age groups; however, guidelines and frameworks are still needed to ensure users' privacy and safety while using them. Suggestions include clearly defining the age of the target population and explicit disclosure of the sharing of users' sensitive data with third parties. In addition, we found an opportunity for apps to better leverage digital affordances for mitigating harm, for personalizing interventions, and for tracking multimodal content. The study further demonstrated the need to consider potential risks while using depression apps, including the use of nonvalidated screening tools, tracking negative moods or thinking patterns, and exposing users to negative emotional expression content., (©Chengcheng Qu, Corina Sas, Claudia Daudén Roquet, Gavin Doherty. Originally published in JMIR Mental Health (http://mental.jmir.org), 24.01.2020.)

Classification of tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as by-product of off-target reads. For the extraction of the target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With three datasets, phylogenetic relationships were reconstructed using both concatenation and coalescent approaches. Phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Nuclear and plastid tree topologies are mostly congruent with a very limited number of incongruent nodes. Based on the well-solved phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. In addition, we further updated the temporal framework for origin and diversification of these subtribes. Our results highlight the power of Hyb-Seq over Sanger sequencing of a few DNA markers in solving phylogenetic relationships of traditionally difficult groups., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The African Austro-temperate Flora stands out by its important species richness. A distinctive element of this flora is Monsonia (Geraniaceae), mostly found in the Namib-Karoo but also in the Natal-Drakensberg, the Somalian Zambezian and the Saharo-Arabian regions. Here, we reconstruct the evolution and biogeographic history of Monsonia based on nuclear and plastid markers, and examine the role of morphological and niche evolution in its diversification using species distribution modeling and macroevolutionary models. Our results indicate that Monsonia first diversified in the Early Miocene c.21 Ma, coinciding with the start of desertification in southwestern Africa. An important diversification occurred c. 4-6 Ma, after a general cooling trend in western South Africa and the rising of the Eastern African Mountains. The resulting two main lineages of Monsonia are constituted by: (1) Namib-Karoo succulents, and (2) herbs of the Natal-Drakensberg plus three species that further colonised steppes in north and eastern Africa. The highest diversity of Monsonia is found in the Namib-Karoo coastal belt, within a mosaic-like habitat structure. Diversification was likely driven by biome shifts and key innovations such as water-storing succulent stems and anemochorous fruits. In contrast, and unlike other arid-adapted taxa, all species of Monsonia share a C 3 metabolism.

Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research., (© The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

The majority of herbivorous insects are specialized feeders restricted to a plant family, genus, or species. The evolution of specialized insect-plant interactions is generally considered to be a result of trade-offs in fitness between possible hosts. Through the course of natural selection, host plants that maximize insect fitness should result in optimal, specialized, insect-plant associations. However, the extent to which insects are tracking plant phylogeny or key plant traits that act as herbivore resistance or acceptance characters is uncertain. Thus, with regard to the evolution of host plant specialization, we tested if insect performance is explained by phylogenetic relatedness of potential host plants, or key plant traits that are not phylogenetically related. We tested the survival (naive first instar to adult) of the oligophagous leaf-feeding beetle, Cassida rubiginosa, on 16 selected representatives of the Cardueae tribe (thistles and knapweeds), including some of the worst weeds in temperate grasslands of the world in terms of the economic impacts caused by lost productivity. Leaf traits (specific leaf area, leaf pubescence, flavonoid concentration, carbon and nitrogen content) were measured as explanatory variables and tested in relation to survival of the beetle, and the phylogenetic signal of the traits were examined. The survival of C. rubiginosa decreased with increasing phylogenetic distance from the known primary host plant, C. arvense, suggesting that specialization is a conserved character, and that insect host range, to a large degree is constrained by evolutionary history. The only trait measured that clearly offered some explanatory value for the survival of C. rubiginosa was specific leaf area. This trait was not phylogenetically dependant, and when combined with phylogenetic distance from C. arvense gave the best model explaining C. rubiginosa survival. We conclude that the specialization of the beetle is explained by a combination of adaptation to an optimal host plant over evolutionary time, and key plant traits such as specific leaf area that can restrict or broaden host utilization within the Cardueae lineage. The phylogenetic pattern of C. rubiginosa fitness will aid in predicting the ability of this biocontrol agent to control multiple Cardueae weeds.

This study investigated pitch perception and production in speech and music in individuals with congenital amusia (a disorder of musical pitch processing) who are native speakers of Cantonese, a tone language with a highly complex tonal system. Sixteen Cantonese-speaking congenital amusics and 16 controls performed a set of lexical tone perception, production, singing, and psychophysical pitch threshold tasks. Their tone production accuracy and singing proficiency were subsequently judged by independent listeners, and subjected to acoustic analyses. Relative to controls, amusics showed impaired discrimination of lexical tones in both speech and non-speech conditions. They also received lower ratings for singing proficiency, producing larger pitch interval deviations and making more pitch interval errors compared to controls. Demonstrating higher pitch direction identification thresholds than controls for both speech syllables and piano tones, amusics nevertheless produced native lexical tones with comparable pitch trajectories and intelligibility as controls. Significant correlations were found between pitch threshold and lexical tone perception, music perception and production, but not between lexical tone perception and production for amusics. These findings provide further evidence that congenital amusia is a domain-general language-independent pitch-processing deficit that is associated with severely impaired music perception and production, mildly impaired speech perception, and largely intact speech production.

Whether the success of alien species can be explained by their functional or phylogenetic characteristics remains unresolved because of data limitations, scale issues and weak quantifications of success. Using permanent grasslands across France (50 000 vegetation plots, 2000 species, 130 aliens) and building on the Rabinowitz's classification to quantify spread, we showed that phylogenetic and functional similarities to natives were the most important correlates of invasion success compared to intrinsic functional characteristics and introduction history. Results contrasted between spatial scales and components of invasion success. Widespread and common aliens were similar to co-occurring natives at coarse scales (indicating environmental filtering), but dissimilar at finer scales (indicating local competition). In contrast, regionally widespread but locally rare aliens showed patterns of competitive exclusion already at coarse scale. Quantifying trait differences between aliens and natives and distinguishing the components of invasion success improved our ability to understand and potentially predict alien spread at multiple scales., (© 2015 John Wiley & Sons Ltd/CNRS.)

The Achillea millefolium aggregate is one of the most diverse polyploid complexes of the Northern hemisphere and has its western Eurasian boundary in the Iberian Peninsula. Four ploidy levels have been detected in A. millefolium, three of which have already been found in Iberia (diploid, hexaploid and octoploid), and a fourth (tetraploid) reported during the preparation of this paper. We collected a sample from 26 Iberian populations comprising all ploidy levels, and we used microsatellite markers analyzed as dominant in view of the high ploidy levels. Our goals were to quantify the genetic diversity of A. millefolium in the Iberian Peninsula, to elucidate its genetic structure, to investigate the differences in ploidy levels, and to analyse the dispersal of the species. The lack of spatial genetic structure recovered is linked to both high levels of gene flow between populations and to the fact that most genetic variability occurs within populations. This in turn suggests the existence of a huge panmictic yarrow population in the Iberian Peninsula. This is consistent with the assumption that recent colonization and rapid expansion occurred throughout this area. Likewise, the low levels of genetic variability recovered suggest that bottlenecks and/or founder events may have been involved in this process, and clonal reproduction may have played an important role in maintaining this genetic impoverishment. Indeed, the ecological and phenologic uniformity present in the A. millefolium agg. in Iberia compared to Eurasia and North America may be responsible for the low number of representatives of this complex of species present in the Iberian Peninsula. The low levels of genetic differentiation between ploidy levels recovered in our work suggest the absence of barriers between them.

Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.

Climate and land cover changes are important drivers of the plant species distributions and diversity patterns in mountainous regions. Although the need for a multifaceted view of diversity based on taxonomic, functional and phylogenetic dimensions is now commonly recognized, there are no complete risk assessments concerning their expected changes. In this paper, we used a range of species distribution models in an ensemble-forecasting framework together with regional climate and land cover projections by 2080 to analyze the potential threat for more than 2,500 plant species at high resolution (2.5 km × 2.5 km) in the French Alps. We also decomposed taxonomic, functional and phylogenetic diversity facets into α and β components and analyzed their expected changes by 2080. Overall, plant species threats from climate and land cover changes in the French Alps were expected to vary depending on the species' preferred altitudinal vegetation zone, rarity, and conservation status. Indeed, rare species and species of conservation concern were the ones projected to experience less severe change, and also the ones being the most efficiently preserved by the current network of protected areas. Conversely, the three facets of plant diversity were also projected to experience drastic spatial re-shuffling by 2080. In general, the mean α-diversity of the three facets was projected to increase to the detriment of regional β-diversity, although the latter was projected to remain high at the montane-alpine transition zones. Our results show that, due to a high-altitude distribution, the current protection network is efficient for rare species, and species predicted to migrate upward. Although our modeling framework may not capture all possible mechanisms of species range shifts, our work illustrates that a comprehensive risk assessment on an entire floristic region combined with functional and phylogenetic information can help delimitate future scenarios of biodiversity and better design its protection.

Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape.

Aim: Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales., Location: European Alps., Methods: We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub-dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α-diversities of local communities, and statistics commonly used together with null models in order to infer non-random diversity patterns (i.e. phylogenetic clustering versus over-dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses., Results: Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over-dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over-dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients., Main Conclusions: Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.

Aim: We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians, to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously., Location: Europe., Methods: Phylogenetic (QE PD ) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10' resolution. We determined the regional relationship between QE PD and SD for each taxa with a spatial regression model and used the tails of the residuals (QE RES ) distribution to identify areas of higher and lower QE PD than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson's correlation. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QE RES value of the same sign for the 3 groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape., Results: QE RES patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QE RES are unequally represented within PAs: areas with higher QE PD than predicted are better covered than expected, while low QE PD areas are undersampled., Main Conclusions: Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.

Aim: The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components., Location: Europe., Methods: From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence., Results: In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches., Main Conclusions: Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on different niche components for all bird species.

Our understanding of processes that led to biogeographic disjunct patterns of plant lineages in Macaronesia, North Africa and Socotra remains poor. Here, we study a group of Campanula species distributed across these areas integrating morphological and reproductive traits with phylogenetic and phylogeographic data based on the obtention of sequences for 4 highly variable cpDNA regions and AFLP data. The phylogeny obtained shows a sister relationship between Campanula jacobaea (endemic to Cape Verde Islands) and C. balfourii (endemic to Socotra), thus revealing a striking disjunct pattern (8300 km). These species diverged around 1.0 Mya; AFLP and haplotype data suggest that no genetic interchange has occurred since then. Their closest taxon, C. hypocrateriformis, is endemic to SW Morocco. The archipelagos of Macaronesia and Socotra have probably acted as refugia for North-African species, leading to speciation through isolation. Although C. balfourii has a restricted distribution, its genetic variability suggests that its populations have suffered no bottlenecks. C. jacobaea is also genetically rich and its distribution across Cape Verde Islands seems to have been influenced by the NE-SW trade winds, which may also have favoured the admixture found among the populations of the three southern islands. Floral features of the morphologically hypervariable C. jacobaea were also measured to assess whether the taxon C. bravensis, described for some of the southeast populations of C. jacobaea, corresponds to a different evolutionary entity. We show that morphological variation in C. jacobaea does not correspond to any genetic or geographic group., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Aim: We still have limited understanding of the contingent and deterministic factors that have fostered the evolutionary success of some species lineages over others. We investigated how the interplay of intercontinental migration and key innovations promoted diversification of the genus Androsace ., Location: Mountain ranges and cold steppes of the Northern Hemisphere., Methods: We reconstructed ancestral biogeographical ranges at regional and continental scales by means of a dispersal-extinction-cladogenesis analysis using dated Bayesian phylogenies and contrasting two migration scenarios. Based on diversification analyses under two frameworks, we tested the influence of life form on speciation rates and whether diversification has been diversity-dependent., Results: We found that three radiations occurred in this genus, at different periods and on different continents, and that life form played a critical role in the history of Androsace . Short-lived ancestors first facilitated the expansion of the genus' range from Asia to Europe, while cushions, which appeared independently in Asia and Europe, enhanced species diversification in alpine regions. One long-distance dispersal event from Europe to North America led to the diversification of the nested genus Douglasia . We found support for a model in which speciation of the North American-European clade is diversity-dependent and close to its carrying capacity, and that the diversification dynamics of the North American subclade are uncoupled from this and follow a pure birth process., Main Conclusions: The contingency of past biogeographical connections combined with the evolutionary determinism of convergent key innovations may have led to replicated radiations of Androsace in three mountain regions of the world. The repeated emergence of the cushion life form was a convergent key innovation that fostered radiation into alpine habitats. Given the large ecological similarity of Androsace species, allopatry may have been the main mode of speciation.

The last decades have seen an upsurge in ecological studies incorporating phylogenetic information with increasing species samples, motivated by the common conjecture that species with common ancestors should share some ecological characteristics due to niche conservatism. This has been carried out using various methods of increasing complexity and reliability: using only taxonomical classification; constructing supertrees that incorporate only topological information from previously published phylogenies; or building supermatrices of molecular data that are used to estimate phylogenies with evolutionary meaningful branch lengths. Although the latter option is more informative than the others, it remains under-used in ecology because ecologists are generally unaware of or unfamiliar with modern molecular phylogenetic methods. However, a solid phylogenetic hypothesis is necessary to conduct reliable ecological analysis integrating evolutive aspects. Our aim here is to clarify the concepts and methodological issues associated with the reconstruction of dated megaphylogenies, and to show that it is nowadays possible to obtain accurate and well sampled megaphylogenies with informative branch-lengths on large species samples. This is possible thanks to improved phylogenetic methods, vast amounts of molecular data available from databases such as Genbank, and consensus knowledge on deep phylogenetic relationships for an increasing number of groups of organisms. Finally, we include a detailed step-by-step workflow pipeline (Supplementary material), from data acquisition to phylogenetic inference, mainly based on the R environment (widely used by ecologists) and the use of free web-servers, that has been applied to the reconstruction of a species-level phylogeny of all breeding birds of Europe.

Relatively, few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life-history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal and that they evolved relatively recently and punctually. Models of niche evolution fitted onto phylogenies show that the cushion life form has been a key innovation providing the opportunity to occupy extremely cold environments, thus contributing to rapid climatic niche diversification in the genus Androsace s.l. We then propose a plausible scenario for the adaptation of plants to alpine habitats., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

Many species are projected to become vulnerable to twenty-first-century climate changes, with consequent effects on the tree of life. If losses were not randomly distributed across the tree of life, climate change could lead to a disproportionate loss of evolutionary history. Here we estimate the consequences of climate change on the phylogenetic diversities of plant, bird and mammal assemblages across Europe. Using a consensus across ensembles of forecasts for 2020, 2050 and 2080 and high-resolution phylogenetic trees, we show that species vulnerability to climate change clusters weakly across phylogenies. Such phylogenetic signal in species vulnerabilities does not lead to higher loss of evolutionary history than expected with a model of random extinctions. This is because vulnerable species have neither fewer nor closer relatives than the remaining clades. Reductions in phylogenetic diversity will be greater in southern Europe, and gains are expected in regions of high latitude or altitude. However, losses will not be offset by gains and the tree of life faces a trend towards homogenization across the continent.

We reconstruct here the spatial and temporal evolution of the Campanula alliance in order to better understand its evolutionary history. To increase phylogenetic resolution among major groups (Wahlenbergieae-Campanuleae), new sequences from the rbcL region were added to the trnL-F dataset obtained in a previous study. These phylogenies were used to infer ancestral areas and divergence times in Campanula and related genera using a Bayesian approach to molecular dating and dispersal-vicariance analyses that takes into account phylogenetic uncertainty. The new phylogenetic analysis confirms Platycodoneae as the sister group of Wahlenbergieae-Campanuleae, the two last ones inter-graded into a well-supported clade. Biogeographic and dating analyses suggest that Western Asia and the Eastern Mediterranean have played a major role as centers of migration and diversification within the Campanula alliance, probably in relation to the intense orogenic activity that took place in this region during the Late Neogene, and that could have promoted isolation and allopatric speciation within lineages. Diversification rates within several Campanula lineages would have increased at the end of the Miocene, coinciding with the Messinian Stage. Strong selective pressures from climate changes and the expansion of mountainous regions during this period are suggested to explain the adaptation to drought, cold or disturbed environments observed in many Campanula species. Several independent long-distance dispersal events to North America are inferred within the Rapunculus clade, which seem to be related to high ploidy levels.